joshuagryphon / plastid Goto Github PK
View Code? Open in Web Editor NEWPosition-wise analysis of sequencing and genomics data
Home Page: https://plastid.readthedocs.io
License: Other
Position-wise analysis of sequencing and genomics data
Home Page: https://plastid.readthedocs.io
License: Other
Hi Plastid team,
I have found a lot of the functionality provided by plastid very useful, but I got frustratingly stuck today when I was trying to run metagene count on data originating from a stranded protocol that produces reads on the opposite of the original strand. I know in your FAQ you suggest reverse-complementing the reads and re-aligning them, but honestly I feel like this is a lot more work than necessary, especially for a big project with many samples.
This issue was almost a deal-breaker for me, but then I realized I could get the same effect by simply reversing the strand of all of my window annotations in my ROI file. I did it with sed, but it would seem to be a pretty straightforward feature to add as a parameter in the actual command, either at the stage of generating the ROI or on the fly during counting. Such a feature would be a relatively easy way to expand usage of plastid by supporting a large number of users with this type of data.
Thanks!
Sarah
PLACEHOLDER: this ticket must be rewritten/edited before work begins.
Python 3.8 was released on October 14 2019. plastid
may require updates to function under Python 3.8
At present, tests for plastid
cannot be tested under Python 3.8 due to a blocking issue with Pysam.
(C:\Users\sunny\Anaconda3) C:\Users\sunny\Documents>cd surprise
(C:\Users\sunny\Anaconda3) C:\Users\sunny\Documents\surprise>python setup.py install
C:\Users\sunny\Anaconda3\lib\site-packages\setuptools\dist.py:360: UserWarning: The version specified ('latest') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.
"details." % self.metadata.version
running install
running bdist_egg
running egg_info
writing scikit_surprise.egg-info\PKG-INFO
writing dependency_links to scikit_surprise.egg-info\dependency_links.txt
writing entry points to scikit_surprise.egg-info\entry_points.txt
writing requirements to scikit_surprise.egg-info\requires.txt
writing top-level names to scikit_surprise.egg-info\top_level.txt
reading manifest file 'scikit_surprise.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'scikit_surprise.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
running build_ext
error: [WinError 2] The system cannot find the file specified
I have upgraded cython, pysam, and numpy.
jfreimer@Mason: ~/build-conda/plastid> pip install --upgrade numpy pysam cython
Requirement already up-to-date: numpy in /N/home/j/f/jfreimer/Mason/miniconda/lib/python2.7/site- packages
Requirement already up-to-date: pysam in /N/home/j/f/jfreimer/Mason/miniconda/lib/python2.7/site-packages
Requirement already up-to-date: cython in /N/home/j/f/jfreimer/Mason/miniconda/lib/python2.7/site-packages
However, I get the following error when I try to install plastid:
jfreimer@Mason: ~/build-conda/plastid> pip install plastid
Collecting plastid
Using cached plastid-0.4.4.tar.gz
Complete output from command python setup.py egg_info:
*** IMPORTANT INSTALLATION INFORMATION ***
plastid setup requires numpy>=1.9.0, pysam>=0.8.4, and cython>=0.22 to be preinstalled. Please
install these via pip, and retry:
$ pip install --upgrade numpy pysam
$ pip install plastid
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-2_hiEj/plastid
The GFF3_TranscriptAssembler
(and presumably other pieces of code) are not compatible with a change made to BioPython 1.78. Namely, the removal of the Bio.Alphabet
module. This page (https://biopython.org/wiki/Alphabet) has more information, but TL;DR, just remove Bio.Alphabet
and most code will still work.
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.
Hello,
I tried to install plastid in environment conda whith pysam, cython et numpy.
When I installed with pip3 (python3.8) the plastid package (v0.5.1) everithing was fine.
But when I try to used this package, I have this error
File "/usr/local/lib/python3.8/dist-packages/plastid/genomics/genome_array.py", line 215, in
from plastid.genomics.map_factories import *
File "plastid/genomics/map_factories.pyx", line 1, in init plastid.genomics.map_factories
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'PileupColumn'
Do you know, where come from my issue?
Thanks a lot in advance,
Hi,
First of all, thank you for developing such a great tool.
It is easy to use and very helpful for my analysis.
I'd like to discuss my procedure for P-site estimation using stop codon peaks, not initiation peaks.
I am analyzing a ribosome profiling data, but it shows diminished initiation peaks due to poor stress response to lysis. So the P-site estimation using the initiation peaks generated noisy results.
Thus, I tried the P-site estimation using stop codon peaks.
Your tutorial mentions it but suggests using another way instead of psite script.
(http://plastid.readthedocs.io/en/latest/examples/p_site.html#id13)
but I think- it could be accomplished by simply,
I think this is an easier way and actually, I found some peaks at 16~17nt for my data.
N. Ingolia's Sciences paper (Sciences 2009) also used this estimation. (See fig. 2B in the paper)
http://science.sciencemag.org/content/324/5924/218.figures-only
I look forward to hearing from you whether it makes sense or not.
Please correct me if I am wrong.
Thanks.
YY.
It seems there is an issue with the regular expression here: https://github.com/joshuagryphon/plastid/blob/master/plastid/util/io/openers.py#L253
When conda packages are built and tested, the paths can be rather long and it seems that this is hanging. I'm not quite sure what the intent of the code is, but I suspect it could be simplified using some os.path
functions.
Hi Joshua,
Thanks for helping with my previous post re: mapfactories not working. Your workaround was great. This is less of an 'issue' and hopefully more of a discussion.
My main question is why and when to use 'centered' based read mapping. Following along in your docs, it appears this normalization is used for RNA-seq data specifically, when manipulating mapping dynamics for downstream analyses.
My next question is under what circumstances would you want to 'nibble' reads as you mapped them? The only thing I can come up with is to increase your signal after reducing it substantially with fractional counting mandated by 'centered' mapping.
Lastly, and a bit of a switch in topics, what would your workflow look like to identify the proportion of various start sites used in two different conditions in riboseq data, especially if alt start sites are located in 5' UTRs? I know that plastid likely contains all of the necessary tools to ask this question, but I am having trouble conceptualizing where to begin.
My best guess is to use the segment chain and genomic segment functionality as well as the 'get_counts' method combined with some type of sub-setting command to specifically target AUGs, NUGs, etc. If you could give me a big picture idea here, that would be super helpful!
Thanks for your time and attention. Really enjoying learning how to use Plastid and all of its functionality!
Respectfully,
Brad
A number of aligners are moving to CRAM from BAM. Because Pysam includes CRAM support, plastid
could support these fairly easily by:
adjusting argument parsers in plastid.util.scriptlib.argparsers
minor changes to file handling/opening BAMGenomeArray
Hello All,
This script does not run on my new linux box (plastid 0.4.8 py37h84994c4_4 bioconda; numpy 1.18.1) but runs on my old linux box (plastid 0.4.8 py27_0 bioconda; numpy 1.14.1) when modified for the directory structure there. It gives the float object error for phase_by_size - and another also another error - on the new box. Advice gratefully appreciated. Thank you.
Script:
for i in *Coord.out.bam
do samtools index $i
done
for i in Coord.out.bam
do psite /media/mrbmk1000/data/ms-pool01/annotationdb/cneoformans/FungDB-38_Cneoformans_cds_start200_rois.txt ${i%.} --min_length 16 --max_length 34 --require_upstream --count_files $i
done
for i in Coord.out.bam
do phase_by_size /media/mrbmk1000/data/ms-pool01/annotationdb/cneoformans/FungDB-38_Cneoformans_cds_start200_rois.txt ${i%.}
--count_files $i
--fiveprime --offset 12
--codon_buffer 5
--min_length 16 --max_length 34
done
New linux box:
(plastid) mrbmk1000@rbmk1000-home-linux:/media/mrbmk1000/data/ms-pool01/C_neoformans/ribo-seq/phasing$ bash ms-pool01_lazy_psites_cneoformans-200min16max34.sh*
RuntimeWarning
pysam.libcalignedsegment.PileupColumn size changed, may indicate binary
incompatibility. Expected 72 from C header, got 88 from PyObject
in /home/mrbmk1000/miniconda3/envs/plastid/lib/python3.7/importlib/_bootstrap.py, line 219:
217 module code)
218 """
219 return f(*args, **kwds)
RuntimeWarning
pysam.libcalignedsegment.PileupColumn size changed, may indicate binary
incompatibility. Expected 72 from C header, got 88 from PyObject
in /home/mrbmk1000/miniconda3/envs/plastid/lib/python3.7/importlib/_bootstrap.py, line 219:
217 module code)
218 """
219 return f(*args, **kwds)
phase_by_size [2020-04-16 16:25:16]: Counted 17318765 total reads.
phase_by_size [2020-04-16 16:25:16]: Counted 1 ROIs ...
Traceback (most recent call last):
File "/home/mrbmk1000/miniconda3/envs/plastid/bin/phase_by_size", line 11, in
load_entry_point('plastid==0.4.8', 'console_scripts', 'phase_by_size')()
File "/home/mrbmk1000/miniconda3/envs/plastid/lib/python3.7/site-packages/plastid/bin/phase_by_size.py", line 190, in main
counts = counts.reshape((len(counts)/3,3))
TypeError: 'float' object cannot be interpreted as an integer
Script running fine on old linux box with same data:
bp-data01@bp-data01:/bp-pool01/c_neoformans/ribo_seq/phasing$ ./lazy_psites_cneoformans-200min16max34.sh*
psite [2020-04-11 15:01:32]: Opening ROI file /bp-pool01/annotationdb/cneoformans/FungDB-38_Cneoformans_cds_start200_rois.txt ...
psite [2020-04-11 15:01:33]: Opening count files rbmk1000-4-59-1_S1_L00X_R1_001_trimmed_811_final_Aligned.sortedByCoord.out.bam ...
psite [2020-04-11 15:01:33]: Counted 17318765 total reads.
psite [2020-04-11 15:01:33]: Counted 1 ROIs ...
psite [2020-04-11 15:01:40]: Counted 1001 ROIs ...
psite [2020-04-11 15:01:48]: Counted 2001 ROIs ...
psite [2020-04-11 15:01:54]: Counted 3001 ROIs ...
psite [2020-04-11 15:02:08]: Counted 4001 ROIs ...
psite [2020-04-11 15:02:14]: Counted 5001 ROIs ...
psite [2020-04-11 15:02:22]: Counted 6001 ROIs ...
psite [2020-04-11 15:02:28]: Counted 6841 ROIs total.
psite [2020-04-11 15:02:34]: Plotting and determining offsets ...
psite [2020-04-11 15:02:34]: Writing offset table to rbmk1000-4-59-1_S1_L00X_R1_001_trimmed_811_final_Aligned.sortedByCoord.out_p_offsets.txt ...
psite [2020-04-11 15:02:34]: Saving plot to rbmk1000-4-59-1_S1_L00X_R1_001_trimmed_811_final_Aligned.sortedByCoord.out_p_offsets.png ...
psite [2020-04-11 15:02:34]: Done.
phase_by_size [2020-04-11 15:02:35]: Counted 17318765 total reads.
phase_by_size [2020-04-11 15:02:35]: Counted 1 ROIs ...
phase_by_size [2020-04-11 15:02:39]: Counted 1001 ROIs ...
phase_by_size [2020-04-11 15:02:44]: Counted 2001 ROIs ...
phase_by_size [2020-04-11 15:02:48]: Counted 3001 ROIs ...
phase_by_size [2020-04-11 15:02:56]: Counted 4001 ROIs ...
phase_by_size [2020-04-11 15:03:00]: Counted 5001 ROIs ...
phase_by_size [2020-04-11 15:03:04]: Counted 6001 ROIs ...
phase_by_size [2020-04-11 15:03:08]: Counted 6841 ROIs total.
phase_by_size [2020-04-11 15:03:08]: Saving phasing table to rbmk1000-4-59-1_S1_L00X_R1_001_trimmed_811_final_Aligned.sortedByCoord.out_phasing.txt ...
phase_by_size [2020-04-11 15:03:08]: Plotting to rbmk1000-4-59-1_S1_L00X_R1_001_trimmed_811_final_Aligned.sortedByCoord.out_phasing.png ...
Two users have reported that Plastid passes installation, but fails during runtime on OSX. This appears to be conda-independent, and occurs even when installing inside virtualenv
. After a successful install, import plastid
yields:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/username/env/lib/python2.7/site-packages/plastid/__init__.py", line 40, in <module>
from plastid.genomics.roitools import (GenomicSegment,
ImportError: dlopen(/Users/username/env/lib/python2.7/site-packages/plastid/genomics/roitools.so, 2): Library not loaded: @rpath/pysam/libctabixproxies.so
Referenced from: /Users/username/env/lib/python2.7/site-packages/plastid/genomics/roitools.so
Reason: image not found
Collecting more information
I am running into issues attempting to generate ROIs for a p-site offset analysis on e. coli. The generated ROIs do not include any upstream region, and the "alignmnet_offset" seems to always be set to the value of the --upstream
parameter. I've used various forms of annotation, but here is an example using the RefSeq GTF files from UCSC:
region_id window_size region masked alignment_offset zero_point
b0001 100 chr:189-239(+) na 50 50
b0002 100 chr:336-386(+) na 50 50
Plastid 0.4.9 contains many deprecated features (largely in plastid.util.scriptlib.argparsers
) that are scheduled to be removed in Plastid 0.5.0. These need to be removed, and tests for the deprecated code migrated to the replacement code.
Dear Plastid Team,
I am working through the tutorial for the metagene analysis and have come up with an error that neither me or our IT department was able to solve. The metatgene_generate command runs successfully and I generated ROI files. However, the metagene count command generates the following error. I would appreciate any assistance or guidance in solving this problem.
-James
metagene [2018-07-09 18:29:33]: Opening ROI file merlin_cds_start_rois.txt ...
Traceback (most recent call last):
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 3064, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'zero_point'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/apps/plastid/0.4.8/bin/metagene", line 11, in
load_entry_point('plastid==0.4.8', 'console_scripts', 'metagene')()
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/plastid/bin/metagene.py", line 1188, in main
do_count(args,al,pp,printer)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/plastid/bin/metagene.py", line 821, in do_count
norm_start, norm_end = _get_norm_region(roi_table, args)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/plastid/bin/metagene.py", line 744, in _get_norm_region
flank_upstream = roi_table["zero_point"][0]
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/frame.py", line 2688, in getitem
return self._getitem_column(key)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/frame.py", line 2695, in _getitem_column
return self._get_item_cache(key)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/generic.py", line 2486, in _get_item_cache
values = self._data.get(item)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/internals.py", line 4115, in get
loc = self.items.get_loc(item)
File "/usr/local/Anaconda/envs_app/plastid/0.4.8/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 3066, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'zero_point'
Hi,
I am getting this error when running psite
:
psite -q my_rois.txt test --min_length 22 --max_length 34 --require_upstream --count_files harr.bam
psite [2020-10-30 10:19:10]: Opening count files harr.bam ...
psite [2020-10-30 10:19:10]: Counted 942136 total reads.
psite [2020-10-30 10:19:10]: Counted 1 ROIs ...
psite [2020-10-30 10:19:11]: Counted 1001 ROIs ...
psite [2020-10-30 10:19:11]: Counted 2001 ROIs ...
psite [2020-10-30 10:19:12]: Counted 3001 ROIs ...
psite [2020-10-30 10:19:13]: Counted 4001 ROIs ...
psite [2020-10-30 10:19:13]: Counted 5001 ROIs ...
psite [2020-10-30 10:19:14]: Counted 6001 ROIs ...
psite [2020-10-30 10:19:15]: Counted 7001 ROIs ...
psite [2020-10-30 10:19:15]: Counted 8001 ROIs ...
psite [2020-10-30 10:19:16]: Counted 9001 ROIs ...
psite [2020-10-30 10:19:17]: Counted 10001 ROIs ...
psite [2020-10-30 10:19:18]: Counted 11001 ROIs ...
psite [2020-10-30 10:19:18]: Counted 12001 ROIs ...
Traceback (most recent call last):
File "/home/user/anaconda2/envs/bin/psite", line 8, in
sys.exit(main())
File "/home/user/anaconda2/envs/lib/python2.7/site-packages/plastid/bin/psite.py", line 345, in main
printer=printer)
File "/home/user/anaconda2/envs/lib/python2.7/site-packages/plastid/bin/psite.py", line 157, in do_count
roi = SegmentChain.from_str(row["region"])
File "plastid/genomics/roitools.pyx", line 3311, in plastid.genomics.roitools.SegmentChain.from_str
ValueError: too many values to unpack (expected 2)
I've found this error when running Plastid 0.5.1, went back to Plastid 0.4.7 and still happened. I have installed plastid through conda, and this is my environment:
Thank you!
I've created a bioconda recipe for Plastid 0.4.7.
Hopefully this helps users of conda to more easily install and use Plastid. If you'd like, I'd encourage you to include a bioconda badge with the following Markdown in the Readme to help point users to Bioconda.
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/plastid/README.html)
I'd be happy to submit a PR with that (and possibly other) documentation updates regarding bioconda.
Build is silently failing on recently upgraded versions of Ubuntu 18.04, in the sense that build completes, but importing plastid.genomics.map_factories
results in an undefined symbol
:
>>> from plastid import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "plastid/__init__.py", line 45, in <module>
from plastid.genomics.genome_array import (
File "plastid/genomics/genome_array.py", line 215, in <module>
from plastid.genomics.map_factories import *
ImportError: plastid/genomics/map_factories.so: undefined symbol: bgzf_read
sudo apt-get upgrade
in a long timeundefined symbol
smells of an issue with one or more of: the C compiler, header files, or source code. However:
plastid
source code hasn't changedpysam
have changed across versions of pysam
, but:
requirements.txt
) works on computer BThis points to the C compiler or something close to it
This can't be the whole picture:
These tests have been done in virtualenvs
as well as Docker containers:
imported
or cimported
(working versions of all dependencies from computer A, when installed on computer B, triggered same error)setuptools
, pip
, and Cython
more up-to-date on computer A than on computer B. Upgrading on computer B to versions on computer A did not solve problem)Hi,
First I would like to thank you for providing this useful and easy-to-use pipeline. It is a great tool for a biologist like me who has limit ability to write codes. I have used metagene and phase_by_size commands and both work well (maybe a bug with UTR in metagene but I fixed it with a pseudo annotation).
I wonder if you can add a feature to phase_by_size to pull out the phasing data for each gene instead of metagene info grouped by read sizes. That would be super helpful for me to look at frame shifting at single-gene level since I want to check if any gene is frame shifted in my yeast mutants and it cannot be seen in metagene data.
Thank you very much!
Hi,
I am new to ribosomal profiling, plastid is very helpful. I followed your guides on website, in masking genome section, I came across a problem. The command I use:
crossmap -k 26 --offset 12 --mismatches 2
I found that there were many short reads(even 1 base) in the output bed file:
chr10 12 513 chr10:12-513(+) 0 + 12 12 0,0,0 1 501, 0,
chr10 13 514 chr10:13-514(-) 0 - 13 13 0,0,0 1 501, 0,
chr10 539 540 chr10:539-540(+) 0 + 539 539 0,0,0 1 1, 0,
chr10 540 541 chr10:540-541(-) 0 - 540 540 0,0,0 1 1, 0,
chr10 590 593 chr10:590-593(+) 0 + 590 590 0,0,0 1 3, 0,
chr10 591 594 chr10:591-594(-) 0 - 591 591 0,0,0 1 3, 0,
chr10 603 631 chr10:603-631(+) 0 + 603 603 0,0,0 1 28, 0,
chr10 604 632 chr10:604-632(-) 0 - 604 604 0,0,0 1 28, 0,
chr10 694 695 chr10:694-695(+) 0 + 694 694 0,0,0 1 1, 0,
chr10 695 696 chr10:695-696(-) 0 - 695 695 0,0,0 1 1, 0,
chr10 697 698 chr10:697-698(+) 0 + 697 697 0,0,0 1 1, 0,
chr10 698 699 chr10:698-699(-) 0 - 698 698 0,0,0 1 1, 0,
chr10 730 733 chr10:730-733(+) 0 + 730 730 0,0,0 1 3, 0,
chr10 731 734 chr10:731-734(-) 0 - 731 731 0,0,0 1 3, 0,
chr10 764 1534 chr10:764-1534(+) 0 + 764 764 0,0,0 1 770, 0,
chr10 765 1535 chr10:765-1535(-) 0 - 765 765 0,0,0 1 770, 0,
chr10 1656 1819 chr10:1656-1819(+) 0 + 1656 1656 0,0,0 1 163, 0,
chr10 1657 1820 chr10:1657-1820(-) 0 - 1657 1657 0,0,0 1 163, 0,
chr10 1821 1873 chr10:1821-1873(+) 0 + 1821 1821 0,0,0 1 52, 0,
chr10 1822 1874 chr10:1822-1874(-) 0 - 1822 1822 0,0,0 1 52, 0,
chr10 1875 1877 chr10:1875-1877(+) 0 + 1875 1875 0,0,0 1 2, 0,
chr10 1876 1878 chr10:1876-1878(-) 0 - 1876 1876 0,0,0 1 2, 0,
chr10 1986 1987 chr10:1986-1987(+) 0 + 1986 1986 0,0,0 1 1, 0,
chr10 1987 1988 chr10:1987-1988(-) 0 - 1987 1987 0,0,0 1 1, 0,
chr10 2140 2142 chr10:2140-2142(+) 0 + 2140 2140 0,0,0 1 2, 0,
chr10 2141 2143 chr10:2141-2143(-) 0 - 2141 2141 0,0,0 1 2, 0,
chr10 2143 2147 chr10:2143-2147(+) 0 + 2143 2143 0,0,0 1 4, 0,
chr10 2144 2148 chr10:2144-2148(-) 0 - 2144 2144 0,0,0 1 4, 0,
chr10 2198 2200 chr10:2198-2200(+) 0 + 2198 2198 0,0,0 1 2, 0,
chr10 2199 2201 chr10:2199-2201(-) 0 - 2199 2199 0,0,0 1 2, 0,
chr10 2256 2258 chr10:2256-2258(+) 0 + 2256 2256 0,0,0 1 2, 0,
chr10 2257 2259 chr10:2257-2259(-) 0 - 2257 2257 0,0,0 1 2, 0,
chr10 2303 2336 chr10:2303-2336(+) 0 + 2303 2303 0,0,0 1 33, 0,
chr10 2304 2337 chr10:2304-2337(-) 0 - 2304 2304 0,0,0 1 33, 0,
Did I miss some key parameters setting? Is it the right output file? Thanks in advance!
Hi Josh,
i am trying to install plastid in an Ubuntu 14.04.5 environment using python 2.7. All dependencies are installed correctly to my knowledge. During installation the setup fails because the cython compiling of map_factories fails.
kevinklann@pqc-Virtual-Machine:~/Downloads/plastid-0.4.6$ python setup.py install
running install
Could not find .c files. Regenerating via recythonize.
Cythonizing
running recythonize
running clean
clean_c_files: removing /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/map_factories.c ...
clean_c_files: removing /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/c_common.c ...
build_c_from_pyx: regenerating .c files from Cython
/home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/map_factories.pyx: cannot find cimported module 'pysam.calignmentfile'
Compiling /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/map_factories.pyx because it changed.
Compiling /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/roitools.pyx because it changed.
Compiling /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/c_common.pyx because it changed.
Compiling plastid/readers/bbifile.pyx because it changed.
Compiling plastid/readers/bigwig.pyx because it changed.
Compiling plastid/readers/bigbed.pyx because it changed.
[1/6] Cythonizing /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/c_common.pyx
[2/6] Cythonizing /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/map_factories.pyx
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignedSegment
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:134:0: 'pysam/calignmentfile.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
import numpy as np
cimport numpy as np
cimport cython
from pysam.calignmentfile cimport AlignedSegment
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:134:0: 'pysam/calignmentfile/AlignedSegment.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
raise ValueError("Alignment size filter: min read length must be >= 1. Got %s" % min)
self.min_ = min
self.max_ = max
def __call__(self,AlignedSegment read not None):
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:812:22: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
raise ValueError("Alignment size filter: min read length must be >= 1. Got %s" % min)
self.min_ = min
self.max_ = max
def __call__(self,AlignedSegment read not None):
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:812:22: Only Python type arguments can have 'not None'
Error compiling Cython file:
------------------------------------------------------------
...
cdef list reads_out = []
cdef list read_positions
cdef:
AlignedSegment read
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:233:12: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
np.ndarray[LONG_t,ndim=1] count_array = np.zeros(seg_len,dtype=LONG)
long [:] count_view = count_array
list reads_out = []
list read_positions
AlignedSegment read
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:328:12: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
np.ndarray[LONG_t,ndim=1] count_array = np.zeros(seg_len,dtype=LONG)
long [:] count_view = count_array
list reads_out = []
list read_positions
AlignedSegment read
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:422:12: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
int no_offset_length
int do_no_offset_warning = 0
int read_length, offset
long p_site
AlignedSegment read
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:596:12: 'AlignedSegment' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
int min_length = self.min_length
list reads_out = []
int read_length, offset, p_site
AlignedSegment read
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:734:12: 'AlignedSegment' is not a type identifier
warning: plastid/genomics/map_factories.pyx:523:35: Index should be typed for more efficient access
Traceback (most recent call last):
File "setup.py", line 591, in <module>
test_suite = "nose.collector",
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "setup.py", line 437, in run
self.run_command(CYTHONIZE_COMMAND)
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 971, in run_command
cmd_obj.ensure_finalized()
File "/usr/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
self.finalize_options()
File "setup.py", line 485, in finalize_options
extensions = cythonize(ext_modules,compiler_directives=CYTHON_ARGS)
File "/usr/local/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 934, in cythonize
cythonize_one(*args)
File "/usr/local/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 1056, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /home/kevinklann/Downloads/plastid-0.4.6/plastid/genomics/map_factories.pyx
The same is true when i try to install it via pip.
Hope you can help me.
Cheers,
Kevin
Hello,
In installing a conda environment with plastid for a customer (python 3.9.15, plastid 0.6.1, numpy 1.24.1) my customer found that their test "metagene generate -h" failed with "AttributeError: module 'numpy' has no attribute 'int'".
From searching online copycode.org indicates that as of numpy 1.24 support for numpy.float and numpy.int were removed. I've downgraded the conda numpy to 1.23.5 and am waiting to hear back from my customer whether their test is successful with the downgraded version.
I'm not a developer, but I'm guessing it might warrant setting a requirement for plastid/0.6.1 for numpy to be <= 1.23.5.
Thank you.
There were a few useful fixes made since 0.4.8 was released. I was hoping you could release an official version (0.4.9?) with the latest updates.
"sudo pip install numpy pysam cython" command fails with the following error,
....
......
copying htslib/htslib/regidx.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.macosx-10.10-intel-2.7/pysam/include/htslib/htslib
running build_ext
building 'pysam.libchtslib' extension
creating build/temp.macosx-10.10-intel-2.7
creating build/temp.macosx-10.10-intel-2.7/pysam
creating build/temp.macosx-10.10-intel-2.7/htslib
creating build/temp.macosx-10.10-intel-2.7/htslib/cram
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -Ipysam -I. -Ihtslib -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/libchtslib.c -o build/temp.macosx-10.10-intel-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from pysam/libchtslib.c:4:
/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33:10: fatal error: 'stdio.h' file not found
#include <stdio.h>
^
1 error generated.
error: command 'cc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;file='/private/tmp/pip-build-qWGO4X/pysam/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-tPjAoV-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/tmp/pip-build-qWGO4X/pysam/
PLEASE SEE
File "./first_v_second_half_RPF_analysis.py", line 12, in
footprints.set_mapping(StratifiedVariableFivePrimeMapFactory.from_file("/tomato/dev/job/BradW/2C_ribo/data_analysis/plastid_5-24/X3_riboprofile_new.txt"))
NameError: name 'StratifiedVariableFivePrimeMapFactory' is not defined.
Traceback (most recent call last):
File "./first_v_second_half_RPF_analysis.py", line 12, in
footprints.set_mapping(VariableFivePrimeMapFactory.from_file("~/tomato/dev/job/BradW/2C_ribo/data_analysis/plastid_5-24/X3_riboprofile_new.txt"))
File "plastid/genomics/map_factories.pyx", line 560, in plastid.genomics.map_factories.VariableFivePrimeMapFactory.from_file (/tmp/pip-build-z6XyxK/plastid/plastid/genomics/map_factories.c:7162)
TypeError: coercing to Unicode: need string or buffer, type found
when i use star to alignment, i can get the bam file compared to the genome(01Aligned.sortedByCoord.out.bam) and the bam file compared to the transcript(01Aligned.toTranscriptome.out.bam), Which one should I choose for psite script analysis?
thank you!
Hi,
First - thank you so much for sharing this tool! I'm relatively new to the data analysis world, and your tool helped me understand how to deal with my ribosome profiling results.
There is one problem I think I don't understand yet how to approach - specifically, I would like to count ribosome footprints over CDS, but effectively exclude several first and last codons. You do mention this briefly in your tutorial, however I'm not sure how to go about that - should I basically try creating a mask file that would mask the codons for all the transcripts, then use it during "cs generate"? I saw the example on the masking page for creating a mask for codons for a singe transcript in the demo bed file - so I supposed there should be a way to apply this to the whole bed/gtf file?
Thank you,
PC
Hi Joshua!
We've been working on the psite (subprogram) but have encountered an issue and would appreciate
some feedback on how to handle this, since it is not very intuitive:
Here's were we started...
(https://plastid.readthedocs.io/en/latest/examples/p_site.html)
The gtf file was obtained from gramene. We did some filtering by removing cp (chloroplast),
mithocondria (mt), tRNA and rRNA reads.
Our bam file was obtained from STAR after multiple sequential alignments to isolate nuclear genomic reads, and they were sorted in indexed with Samtools:
samtools sort --threads 27 ${in_file} -o sorted_${out_filename}
samtools index ${in_file} -b indexed_${out_filename}
After running the metagene generate on our maize reference and obtaining the *_rois.txt
file required for the next step (psite), we tested on our indexed bam file but encountered
the following warning messages:
"[E::hts_hopen] Failed to open file indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam
[E::hts_open_format] Failed to open file indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam
psite [2018-11-02 09:59:03]: Opening ROI file Zea_mays_orfs_rois.txt ...
psite [2018-11-02 09:59:04]: Opening count files indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam ...
Traceback (most recent call last):
File "/packages/anaconda3/5.1.0/envs/plastid/bin/psite", line 11, in
load_entry_point('plastid==0.4.8', 'console_scripts', 'psite')()
File "/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/bin/psite.py", line 326, in main
ga = ap.get_genome_array_from_args(args,printer=printer)
File "/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/util/scriptlib/argparsers.py", line 572, in get_genome_array_from_args
count_files = [pysam.Samfile(X,"rb") for X in args.count_files]
File "/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/util/scriptlib/argparsers.py", line 572, in
count_files = [pysam.Samfile(X,"rb") for X in args.count_files]
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.cinit
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open
OSError: [Errno 8] could not open alignment file indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam
: Exec format error"
The indexed bam files seem to be ok since we ran Subreads (featureCounts) on them, but for some reason, we cannot run plastid on them (counts_file argument, failed to open)
We appreciate your feedback and look forward to hearing back from you.
Ana and Mandie
Hi Joshua,
EDIT: Just noticed this was reported in #13 , will see if that solves it. Sorry!
I've installed plastid in a virtualenv as explained in your guide but I am getting an ImportError for a pysam library it seems? Do you have an idea what could be going wrong? Cheers!
(plastid_env) 133-33-123-5:~ jmcarter$ python -c "from plastid import *"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/jmcarter/BioUnix/plastid_env/lib/python2.7/site-packages/plastid/__init__.py", line 40, in <module>
from plastid.genomics.roitools import (GenomicSegment,
ImportError: dlopen(/Users/jmcarter/BioUnix/plastid_env/lib/python2.7/site-packages/plastid/genomics/roitools.so, 2): Library not loaded: @rpath/pysam/libctabixproxies.so
Referenced from: /Users/jmcarter/BioUnix/plastid_env/lib/python2.7/site-packages/plastid/genomics/roitools.so
Reason: image not found
Hello,
logging is part of the standard library in python3
having setup.py requires for 'logging' causes problems while logging is grabbed from pypi and as logging module from pypi is python2 syntax.
regards
Eric
Hello,
I'm having an issue running crossmap on the human genome, specifically it seems like when it gets to the unlocalized or unplaced scaffolds. I have limited the dataset by not using the "alt" versions of the chromosomes, but these other scaffolds seem to be having issues within the program causing it to exit out without a response. Have you encountered this problem?
Grant
Hi Plastid team,
I am a beginner in ribosomal profiling and try to use plastid to analyze my data. It is a wonderful tool.
I run the "metagene count" command with the demo data, likes
metagene count merlin_cds_start_rois.txt SRR609197_riboprofile \ --count_files SRR609197_riboprofile_5hr_rep1.bam \ --fiveprime --offset 14 --normalize_over 30 200 \ --min_counts 50 --cmap Blues --title "Metagene demo"
And I got two RuntimeWarning, just like
But I still can get a similar result likes the demo.
Could you help me with this issue?
Thank you
Hi,
I am trying to generate a metagene plot for my samples treated
and untreated
. However I can only generate a plot having one of the samples ( either of them ) as in count
the input bam files get pooled together.
So the output looks as follows for the 'treated
' sample:
How can I add'untreated'
input to this plot to compare their trend for metagene distribution?
Thank you.
Running unit tests under python3.7 elicits this bug, caused by Python 3.7's implementation of PEP 479, which converts StopIteration
exceptions in generators — which, until and including Python 3.6 were the proper way to signal termination of a generator — into RuntimeError
instances.
PEP479 proposes a resolution, of wrapping basically everything in try-except
blocks.
Dear Joshua,
Thanks for this tool, it is a great addition to the software I have been using so far.
I would like to mention two issues I encountered when using plastid:
To circumvent this issue, I used make_wiggle to generate coverage profiles, which I have supplied to get_count_vectors. However, I am also not sure if get_count_vectors can handle these files properly, since it's input formats comprise "BAM,bigwig,bowtie,wiggle" and my current test run only displays the following (after a runtime of >60 minutes) while the process keeps running using a core at 100%:
get_count_vectors [2017-02-08 11:34:48]: Opening wiggle files RPF_sample1 ...
This brings me to the second issue I have encountered.
Kind regards
Hello,
In the doc, the parameter
--gff_transcript_types GFF_TRANSCRIPT_TYPES [GFF_TRANSCRIPT_TYPES ...] GFF3 feature types to include as transcripts, even if no exons are present (for GFF3 only; default: use SO v2.5.3 specification)
and
--mask_gff_transcript_types MASK_GFF_TRANSCRIPT_TYPES [MASK_GFF_TRANSCRIPT_TYPES ...] GFF3 feature types to include as transcripts, even if no exons are present (for GFF3 only; default: use SO v2.5.3 specification)
have exactly same explation. So what's the difference bewteen them? --gff_exon_types and --gff_cds_types also have same problem.
Hey, I wanted to try out plastid but got the following error:
>>> import plastid
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/pkerpedjiev/miniconda3/envs/cenv4/lib/python3.8/site-packages/plastid/__init__.py", line 39, in <module>
from plastid.genomics.roitools import (
ModuleNotFoundError: No module named 'plastid.genomics.roitools'
Any suggestions? I'm in a conda environment, Python 3.8 and installed plastid using pip install plastid
.
Hi,
I used the 'phase_by_size' script and it reports this error in '......../plastid/bin/phase_by_size.py' line 190 , in main:
counts = counts.reshape(len(counts)/3,3)
TypeError: 'float' object cannot be interpreted as an integer
I found it happens because of numpy.reshape (Numpy(1.13.1)) no longer support float as an input, but it works at Numpy 1.11.1. I changed the code and it works.
Hi Josh!
Just installed plastid in a mac os x conda environment and thought I'd post the issues I ran into. Even in the virtual environment pip build failed, I think due to pysam 0.6 being the latest on the defaults conda channel. I updated to the latest pysam I could find (0.9.1, on the bioconda channel), and voila, pip install plastid ran fine.
However, importing plastid raised the following error:
...from plastid.genomics.map_factories import *
File "cfaidx.pxd", line 40, in init plastid.genomics.map_factories (.../plastid/genomics/map_factories.c:24002)
ValueError: pysam.cfaidx.FastaFile has the wrong size, try recompiling
I rolled back to plastid's minimum pysam requirement (0.8.4) and now it's all peachy keen. Thought you'd want to know.
Thanks,
Calvin
Dear all,
I am having problems with the installation and the solutions proposed in the documentation didn't work so far. Your help will be really appreciated.
1st attempt: installing plastid with pip install gave me the following error:
"ERROR: Could not build wheels for plastid, which is required to install pyproject.toml-based projects"
python version: Python 3.7.10; pip version: pip version 22.0.4; Linux distribution: "CentOS Linux 7 (Core)"
2nd attempt: installing plastid in a new conda environment gave me this error:
PackagesNotFoundError: The following packages are not available from current channels:
3rd attempt: installing plastid in a vanilla environment (virtualenv) so that I make sure that there are no conflicts with other packages etc. "ERROR: Could not build wheels for plastid, which is required to install pyproject.toml-based projects"
Is there anything I am missing?? any system library or something like that? a problem with the gcc compiler?
Thank you very much in advance!
Find below the log of one of the installation attempts.
###########################################################################################
Using pip 22.0.4 from /home/lmateo/miniconda3/envs/orfrater/lib/python3.7/site-packages/pip (python 3.7)
Collecting plastid
Downloading plastid-0.6.1.tar.gz (1.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 8.5 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pysam>=0.8.4
Downloading pysam-0.19.0-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.0/15.0 MB 58.4 MB/s eta 0:00:00
Collecting twobitreader>=3.0.0
Downloading twobitreader-3.1.7.tar.gz (9.2 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting biopython>=1.64
Downloading biopython-1.79-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (2.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 12.2 MB/s eta 0:00:00
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/c0/ad/e3c052ed4e0027a8abef0a5e8441a044427d252d17d9aee06d56e62fc698/scipy-1.8.0rc1.tar.gz#sha256=54adf5c1197d6c3de2e131dc71660bb11d4e449aff79c8c231bd05dc6ad307eb (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/29/d2/151a54944b333e465f98804dced31dab1284f3c37b752b9cefa710b64681/scipy-1.8.0rc2.tar.gz#sha256=d73b13eb0452c178f946b4db60b27e400225df02e926609652ed67798054e77d (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/e4/26/83dd1c6378513a6241d984bda9f08c512b6e35fff13fba3acc1b3c195f02/scipy-1.8.0rc3.tar.gz#sha256=7e4f827b37275b1264102f2cc063ba17a40fb858af7a98f63b3b1be2670a34b1 (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/22/78/056cc43e7737811b6f50886788a940f852773dd9804f5365952805db9648/scipy-1.8.0rc4.tar.gz#sha256=bfa5b17b108203c31388d362fe666b96c2f0aa1a094d460aab85440c22e6f22f (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/b4/a2/4faa34bf0cdbefd5c706625f1234987795f368eb4e97bde9d6f46860843e/scipy-1.8.0.tar.gz#sha256=31d4f2d6b724bc9a98e527b5849b8a7e589bf1ea630c33aa563eda912c9ff0bd (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Link requires a different Python (3.7.10 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/26/b5/9330f004b9a3b2b6a31f59f46f1617ce9ca15c0e7fe64288c20385a05c9d/scipy-1.8.1.tar.gz#sha256=9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33 (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
Collecting scipy>=0.15.1
Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 40.1 MB/s eta 0:00:00
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/29/e3/6bd596d81eaf9f5b35398fdac0c535efadd9bbf8d0f859739badf9f90c63/pandas-1.4.0rc0.tar.gz#sha256=c0d453fda0a87d51f5fe65c16a89b64f13a736f4f17c0202cfcff67e6b341a57 (from https://pypi.org/simple/pandas/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/4d/aa/e7078569d20f45e8cf6512a24bf2945698f13a7975650773c01366ea96dc/pandas-1.4.0.tar.gz#sha256=cdd76254c7f0a1583bd4e4781fb450d0ebf392e10d3f12e92c95575942e37df5 (from https://pypi.org/simple/pandas/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/c4/eb/cfa96ba42695b3c28d4864a796d492f188471dd536df7e5e5e0c54b629a6/pandas-1.4.1.tar.gz#sha256=8db93ec98ac7cb5f8ac1420c10f5e3c43533153f253fe7fb6d891cf5aa2b80d2 (from https://pypi.org/simple/pandas/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/5a/ac/b3b9aa2318de52e40c26ae7b9ce6d4e9d1bcdaf5da0899a691642117cf60/pandas-1.4.2.tar.gz#sha256=92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12 (from https://pypi.org/simple/pandas/) (requires-python:>=3.8)
Collecting pandas>=0.17.0
Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 37.2 MB/s eta 0:00:00
Collecting cython>=0.22.0
Downloading Cython-0.29.30-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 43.7 MB/s eta 0:00:00
Collecting termcolor
Downloading termcolor-1.1.0.tar.gz (3.9 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting matplotlib>=1.4.0
Downloading matplotlib-3.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.2/11.2 MB 39.1 MB/s eta 0:00:00
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/7a/7f/5384d4c85a2349bd89ff1c0253bff77c7b617e48af201f2d823fc619189a/numpy-1.22.0rc1.zip#sha256=bc991b3f8ea7c0f6703df2bc23c098cfe6f1a3a5e8a3a901eb6a5619275d53ff (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/a1/4a/8fd68d9a0a9fe5419cdbb697ffc96259fb716bd952c5c64225991add7551/numpy-1.22.0rc2.zip#sha256=01810dc32c5ac4c895b5c0d285497e1eb52038834919f3d2eaddfb9526b20dc9 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/17/d4/d3ac79fca81154e8d3e11232967024f480cfdc87dfeef479803716fb20cb/numpy-1.22.0rc3.zip#sha256=0b5642efe2a36f2191102b44bb95ee1479f14c1adb2d7155303e50b2517e43bc (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/numpy-1.22.0.zip#sha256=a955e4128ac36797aaffd49ab44ec74a71c11d6938df83b1285492d277db5397 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/0a/c8/a62767a6b374a0dfb02d2a0456e5f56a372cdd1689dbc6ffb6bf1ddedbc0/numpy-1.22.1.zip#sha256=e348ccf5bc5235fc405ab19d53bec215bb373300e5523c7b476cc0da8a5e9973 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/e9/6c/c0a8130fe198f27bab92f1b28631e0cc2572295f6b7a31e87efe7448aa1c/numpy-1.22.2.zip#sha256=076aee5a3763d41da6bef9565fdf3cb987606f567cd8b104aded2b38b7b47abf (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/64/4a/b008d1f8a7b9f5206ecf70a53f84e654707e7616a771d84c05151a4713e9/numpy-1.22.3.zip#sha256=dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18 (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Link requires a different Python (3.7.10 not in: '>=3.8'): https://files.pythonhosted.org/packages/f6/d8/ab692a75f584d13c6542c3994f75def5bce52ded9399f52e230fe402819d/numpy-1.22.4.zip#sha256=425b390e4619f58d8526b3dcf656dde069133ae5c240229821f01b5f44ea07af (from https://pypi.org/simple/numpy/) (requires-python:>=3.8)
Collecting numpy>=1.9.4
Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 42.2 MB/s eta 0:00:00
Collecting python-dateutil>=2.7
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 KB 102.7 MB/s eta 0:00:00
Collecting packaging>=20.0
Downloading packaging-21.3-py3-none-any.whl (40 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 KB 53.7 MB/s eta 0:00:00
Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
Downloading fonttools-4.33.3-py3-none-any.whl (930 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 930.9/930.9 KB 66.3 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.4.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 50.2 MB/s eta 0:00:00
Collecting pillow>=6.2.0
Downloading Pillow-9.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 47.6 MB/s eta 0:00:00
Collecting pyparsing>=2.2.1
Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 KB 90.8 MB/s eta 0:00:00
Collecting pytz>=2017.3
Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 KB 50.5 MB/s eta 0:00:00
Collecting typing-extensions
Downloading typing_extensions-4.2.0-py3-none-any.whl (24 kB)
Collecting six>=1.5
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: plastid, twobitreader, termcolor
Building wheel for plastid (pyproject.toml): started
Building wheel for plastid (pyproject.toml): finished with status 'error'
Building wheel for twobitreader (setup.py): started
Building wheel for twobitreader (setup.py): finished with status 'done'
Created wheel for twobitreader: filename=twobitreader-3.1.7-py3-none-any.whl size=9602 sha256=48feed40c805dbbcffafd2fcbc7731b1b7b30f4b3ee9e461f75cd207f46827ae
Stored in directory: /tmp/pip-ephem-wheel-cache-_hfd3tv8/wheels/d7/4f/70/282382e10dc13fd946f157888d9652437b01e3ac4541ac4b4b
Building wheel for termcolor (setup.py): started
Building wheel for termcolor (setup.py): finished with status 'done'
Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4848 sha256=31dede504b8826f170c8c0b1e06eb37fc09f3a70ce4b543f7beae55ea0fb5050
Stored in directory: /tmp/pip-ephem-wheel-cache-_hfd3tv8/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
Successfully built twobitreader termcolor
Failed to build plastid
reformat_transcripts --annotation_files Drosophila_melanogaster.BDGP6.28.100.sorted.gff3 --annotation_format GFF3 --sorted --output_format GTF2 Drosophila_melanogaster.BDGP6.28.100.sorted.gtf2
Traceback (most recent call last):
File "###/opt/anaconda3/envs/plastid/bin/reformat_transcripts", line 11, in
load_entry_point('plastid==0.4.7', 'console_scripts', 'reformat_transcripts')()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 488, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2861, in load_entry_point
return ep.load()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2461, in load
return self.resolve()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2467, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/plastid/init.py", line 44, in
from plastid.genomics.genome_array import (BAMGenomeArray,
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/plastid/genomics/genome_array.py", line 215, in
from plastid.genomics.map_factories import *
File "libchtslib.pxd", line 2530, in init plastid.genomics.map_factories (/anaconda/conda-bld/plastid_1494346258083/work/plastid-0.4.7/plastid/genomics/map_factories.c:26281)
ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80
Hello,
I installed plastid, have updated numpy, pysam and Cython.
when in python I type import plastid
I always get this message:
Traceback (most recent call last):
File "< stdin >", line 1, in < module >
ImportError: No module named 'plastid'
What`s wrong and what can I do with it?
Thanks.
Dear Plastid Team,
I have been using plastid for about a week now. Everything runs fine, no errors. Metagene profile looks representative of regular riboseq data.
However, the .bed file that is returned (after the first 31 lines) when running the metagene generate
function looks like this:
6 41079039 41079164 ENSG00000001167 0 + 41079089 41079090 0,0,0 1 125, 0,
6 46130172 46139783 ENSG00000001561 0 + 46139583 46139584 0,0,0 2 17,233, 0,9378,
4 11399805 11400055 ENSG00000002587 0 - 11400004 11400005 0,0,0 1 250, 0,
17 28355837 28357463 ENSG00000004142 0 - 28357447 28357448 0,0,0 2 39,176, 0,1450,
12 21491532 21499615 ENSG00000004700 0 - 21499569 21499570 0,0,0 2 184,61, 0,8022,
19 35755892 35757009 ENSG00000004776 0 - 35757007 35757008 0,0,0 2 2,199, 0,918,
X 11112018 11114934 ENSG00000004961 0 + 11112060 11112061 0,0,0 2 142,100, 0,2816,
4th line, on what I have checked on .BED file format, would result on a "score" which on this case I would assume would be the ribosome-protected-fragment counts on the selected windows. Is that right?
I then make a .bedgraph file using this command:
$ cut -f1-3,5 my.bed > my.bedgraph
. It looks like this (again, after the first 31 lines):
6 41079039 41079164 0
6 46130172 46139783 0
4 11399805 11400055 0
17 28355837 28357463 0
12 21491532 21499615 0
19 35755892 35757009 0
X 11112018 11114934 0
I would assume that the 3rd line should have some numbers so as to allow visualization into genome browsers or other tools.
Is there something I am doing wrong?
Thank you in advance,
Alexandros
I am trying to install this package locally from source using any of
pip install --user .
pip install --user -e .
pip install --user --global-option="--recythonize" . # since --install-option was removed by pip
but I always get the following error
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting scipy>=0.15.1 (from plastid==0.6.1)
Using cached scipy-1.11.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.3 MB)
Collecting pandas>=0.17.0 (from plastid==0.6.1)
Using cached pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.3 MB)
Requirement already satisfied: matplotlib>=1.4.0 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from plastid==0.6.1) (3.7.2)
Collecting biopython>=1.64 (from plastid==0.6.1)
Using cached biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Collecting twobitreader>=3.0.0 (from plastid==0.6.1)
Using cached twobitreader-3.1.7-py3-none-any.whl
Collecting termcolor (from plastid==0.6.1)
Using cached termcolor-2.3.0-py3-none-any.whl (6.9 kB)
Requirement already satisfied: numpy>=1.9.4 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from plastid==0.6.1) (1.23.5)
Requirement already satisfied: pysam>=0.8.4 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from plastid==0.6.1) (0.21.0)
Requirement already satisfied: cython>=0.22.0 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from plastid==0.6.1) (3.0.0)
Requirement already satisfied: contourpy>=1.0.1 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (4.41.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (1.4.4)
Requirement already satisfied: packaging>=20.0 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (23.1)
Requirement already satisfied: pillow>=6.2.0 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (9.5.0)
Requirement already satisfied: pyparsing<3.1,>=2.3.1 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (3.0.9)
Requirement already satisfied: python-dateutil>=2.7 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from matplotlib>=1.4.0->plastid==0.6.1) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from pandas>=0.17.0->plastid==0.6.1) (2023.3)
Collecting tzdata>=2022.1 (from pandas>=0.17.0->plastid==0.6.1)
Using cached tzdata-2023.3-py2.py3-none-any.whl (341 kB)
Requirement already satisfied: six>=1.5 in /home/moritzloewer/anaconda3/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib>=1.4.0->plastid==0.6.1) (1.16.0)
Building wheels for collected packages: plastid
Building wheel for plastid (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for plastid (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [89 lines of output]
running bdist_wheel
running build
running build_py
copying plastid/genomics/roitools.pyx -> build/lib.linux-x86_64-cpython-310/plastid/genomics
copying plastid/genomics/map_factories.c -> build/lib.linux-x86_64-cpython-310/plastid/genomics
copying plastid/genomics/roitools.c -> build/lib.linux-x86_64-cpython-310/plastid/genomics
copying plastid/genomics/c_common.c -> build/lib.linux-x86_64-cpython-310/plastid/genomics
copying plastid/readers/bigwig.c -> build/lib.linux-x86_64-cpython-310/plastid/readers
copying plastid/readers/bbifile.c -> build/lib.linux-x86_64-cpython-310/plastid/readers
copying plastid/readers/bigbed.c -> build/lib.linux-x86_64-cpython-310/plastid/readers
running build_ext
building 'plastid.genomics.c_common' extension
gcc -pthread -B /home/moritzloewer/anaconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/moritzloewer/anaconda3/include -fPIC -O2 -isystem /home/moritzloewer/anaconda3/include -fPIC -I/home/moritzloewer/Bachelor/plastid/plastid/kent/src/htslib -I/home/moritzloewer/Bachelor/plastid/plastid/kent/src/inc -I/tmp/pip-build-env-i6xqx771/normal/lib/python3.10/site-packages/numpy/core/include -I/tmp/pip-build-env-i6xqx771/normal/lib/python3.10/site-packages/pysam -I/tmp/pip-build-env-i6xqx771/normal/lib/python3.10/site-packages/pysam/include/htslib -I/tmp/pip-build-env-i6xqx771/normal/lib/python3.10/site-packages/pysam/include/samtools -I/home/moritzloewer/anaconda3/include/python3.10 -c /home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/c_common.c -o build/temp.linux-x86_64-cpython-310/home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/c_common.o
gcc -pthread -B /home/moritzloewer/anaconda3/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/home/moritzloewer/anaconda3/lib -Wl,-rpath-link,/home/moritzloewer/anaconda3/lib -L/home/moritzloewer/anaconda3/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/home/moritzloewer/anaconda3/lib -Wl,-rpath-link,/home/moritzloewer/anaconda3/lib -L/home/moritzloewer/anaconda3/lib build/temp.linux-x86_64-cpython-310/home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/c_common.o -lssl -lcrypto -lz -o build/lib.linux-x86_64-cpython-310/plastid/genomics/c_common.cpython-310-x86_64-linux-gnu.so
warning: plastid/genomics/map_factories.pyx:134:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
warning: plastid/genomics/map_factories.pyx:145:0: The 'DEF' statement is deprecated and will be removed in a future Cython version. Consider using global variables, constants, and in-place literals instead. See https://github.com/cython/cython/issues/4310
Error compiling Cython file:
------------------------------------------------------------
...
LONG = np.long
ctypedef np.int_t INT_t
ctypedef np.float_t FLOAT_t
ctypedef np.double_t DOUBLE_t
ctypedef np.long_t LONG_t
^
------------------------------------------------------------
plastid/genomics/map_factories.pyx:154:9: 'long_t' is not a type identifier
warning: plastid/genomics/map_factories.pyx:542:24: Index should be typed for more efficient access
Compiling /home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/map_factories.pyx because it changed.
[1/1] Cythonizing /home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/map_factories.pyx
Traceback (most recent call last):
File "/home/moritzloewer/anaconda3/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/moritzloewer/anaconda3/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/moritzloewer/anaconda3/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 416, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 401, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 476, in <module>
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 107, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-i6xqx771/normal/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 346, in run
self.run_command("build")
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
super().run_command(command)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "<string>", line 398, in run
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/Cython/Distutils/build_ext.py", line 122, in build_extension
new_ext = cythonize(
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-i6xqx771/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /home/moritzloewer/Bachelor/plastid/plastid/plastid/genomics/map_factories.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for plastid
Failed to build plastid
ERROR: Could not build wheels for plastid, which is required to install pyproject.toml-based projects
Alternatively is there a way to be able to import plastid in the python interpreter running in the anaconda environment (where installation succeeded) ?
I downloaded the source from https://files.pythonhosted.org/packages/source/p/plastid/plastid-0.4.6.tar.gz, untarred it and tried to run python setup.py build
in the obtained source directory. This resulted in the following error:
gcc: error: /home/bli/src/plastid-0.4.6/plastid/genomics/c_common.c: No such file or directory
Is there some missing file or some missing building step somewhere?
This is mostly done & gives a 2-3x speedbump in a number of scripts
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.