Chain samples together ('chain_samples.py') about cdna_cupcake

[Magdoll]

Hi @xogur ,

So are you saying get_abundance_post_collapse.py did successfully work and you get a xxxxx.collapsed.abundance.txt? And just the chain_samples.py itself failed?

Would you mind posting the full command for chain_samples.py, your input samples.config and the error message? Also, the first few lines for xxxxx.collapsed.abundance.txt via:

$ head -n 15 xxxxx.collapsed.abundance.txt

[tay45]

Hi Magdoll,

I didn't have any error in the 'get_abundance_post_collapse.py'.

Please take a look at my log for the 'chain_samples.py' and the 'config' and the 'xxxxx.collapsed.abundance.txt' at below. Thank you!

#log of the 'chain_samples.py'
-sh-3.2$ chain_samples.py test.config norm_nfl
Sanity checking. Retrieving PBIDs from /isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.group.txt,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.gff,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.abundance.txt...
Sanity checking. Retrieving PBIDs from /isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.group.txt,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.gff,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.abundance.txt...
Traceback (most recent call last):
File "/opt2/Python-2.7.13/bin/chain_samples.py", line 4, in
import('pkg_resources').run_script('cupcake==3.9', 'chain_samples.py')
File "/opt2/Python-2.7.13/lib/python2.7/site-packages/pkg_resources/init.py", line 743, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/opt2/Python-2.7.13/lib/python2.7/site-packages/pkg_resources/init.py", line 1498, in run_script
exec(code, namespace, namespace)
File "/opt2/Python-2.7.13/lib/python2.7/site-packages/cupcake-3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/chain_samples.py", line 233, in
chain_samples(sample_dirs, sample_names, group_filename, gff_filename, count_filename, args.field_to_use, args.fuzzy_junction, args.allow_5merge, fastq_filename)
File "/opt2/Python-2.7.13/lib/python2.7/site-packages/cupcake-3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/chain_samples.py", line 121, in chain_samples
count_info = read_count_info(count_filename, dirs, field_to_use)
File "/opt2/Python-2.7.13/lib/python2.7/site-packages/cupcake-3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/chain_samples.py", line 111, in read_count_info
return count_header, count_info
NameError: global name 'count_header' is not defined
-sh-3.2$

#'config'
SAMPLE=1;/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3
SAMPLE=2;/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2

GROUP_FILENAME=test.collapsed.group.txt
GFF_FILENAME=test.collapsed.gff
COUNT_FILENAME=test.collapsed.abundance.txt
FASTQ_FILENAME=test.collapsed.rep.fq

#'xxxxx.collapsed.abundance.txt'
-sh-3.2$ head -n 15 test.collapsed.abundance.txt

-----------------

Field explanation

-----------------

count_fl: Number of associated FL reads

count_nfl: Number of associated FL + unique nFL reads

count_nfl_amb: Number of associated FL + unique nFL + weighted ambiguous nFL reads

norm_fl: count_fl / total number of FL reads

norm_nfl: count_nfl / total number of FL + unique nFL reads

norm_nfl_amb: count_nfl_amb / total number of all reads

Total Number of FL reads: 17033

Total Number of FL + unique nFL reads: 20533

Total Number of all reads: 21143

pbid count_fl count_nfl count_nfl_amb norm_fl norm_nfl norm_nfl_amb
-sh-3.2$

[Magdoll]

Hi @xogur ,

It appears a branch merge I did a while back kept coming back to haunt me. It's a bug that I have fixed and is now in v4.1. Let me know.

--Liz

[tay45]

Hi Magdoll,

Thank you very much Magdoll! The error has been fixed and it is working well!

Taehee

-sh-3.2$ chain_samples.py test.config norm_nfl
Sanity checking. Retrieving PBIDs from /isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.group.txt,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.gff,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/tofu2/evaluate_tofu2/collapse3/test.collapsed.abundance.txt...
Sanity checking. Retrieving PBIDs from /isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.group.txt,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.gff,/isi-dcnl/user_data/Seq/pacbio_analysis/thkang/IsoSeq_test/Alzheimer_isoseq/smrtanalysis_3/bax2bam/collapse/collapse2/test.collapsed.abundance.txt...
Chained output written to:
all_samples.chained.gff
all_samples.chained_ids.txt
all_samples.chained_count.txt
all_samples.chained.rep.fq