Contact Details

What happened?

Hi!

I am trying to access the results after client.query using the Bio module instead of parsing the results as a list. In the tutorial you say that "The query result is the same as QueryResult of Bio.", however I can't access the data that way:

ret1 = client.query("GAAGAAGCTGGGATTGGAATGCAGGTCTCTTGCGGGATGTGGTGTGGGAGGAGAATGCACAAATGGACAGAGTGGGGGTTGGGGGCTGGGAAAGAGCTAAGGACCAGGGCAGGAGGGGATTCAAGAGACTGAGTAGGGCAGCTAGCTAGTTCCTGGGAGCTCTTCCCTTGTCATCTCATCAGTTTGGACTCCTCGAACAATTC")

# Command
ret1
# Result
[QueryResult(id='/tmp/tmpdd6dm058', 4 hits)]

# Command
type(ret1)
# Result
list

# Command
type(ret1[0])
# Result
Bio.SearchIO._model.query.QueryResul

# Command
qresults = SearchIO.parse(ret1[0], 'blast-xml') #I tried different formats
qresults
# Result
<generator object parse at 0x2b500bf297a0>

# Command
type(qresults)
# Result
generator

# Command
next(qresults)
# Result
TypeError: expected str, bytes or os.PathLike object, not QueryResult

# Command
qresults[0]
# Result
TypeError: 'generator' object is not subscriptable

# Command
for item in qresults:
    print(item)
# Result
TypeError: expected str, bytes or os.PathLike object, not QueryResult

# Command
for item in qresults:
    type(item)
# Result
TypeError: expected str, bytes or os.PathLike object, not QueryResult

I don't know if I'm doing something wrong, but I tried everything I knew.

Thank you very much! This program is very useful!!!

Best,
Ander

Version

v0.3.4

What platform are you working on?

Linux

Relevant log output

No response

Code of Conduct

• #163

Contact Details

No response

What happened?

A bug happened!

Version

vall

What platform are you working on?

Linux

Relevant log output

s

Code of Conduct

• I agree to follow this project's Code of Conduct

📆 To-do

• parser gfclient result
• parse gfserver query result
• benchmarking multi connection and original version
• test result with original version
• fix build.py to build ssl, hts, maybe libuv when install with pip
• add tool to conda channel
• add tool to pip
• change abort to throw exceptions
• implement twobit2fa
• implement psl2sam
• implement WebUI

📖 Enhance Documentation

• Add comparable command line of BLAT

Add more tools as binding for current ucsc command line tools

https://www.gevent.org/api/gevent.greenlet.html#subclassing-greenlet

What happened?

$ python -c "import pxblat"                                                                                             16:32:11
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/ylk4626/miniforge3/envs/test_pxblat/lib/python3.10/site-packages/pxblat/__init__.py", line 1, in <module>
    from .extc import ClientOption
  File "/Users/ylk4626/miniforge3/envs/test_pxblat/lib/python3.10/site-packages/pxblat/extc/__init__.py", line 1, in <module>
    from .._extc.cppbinding import *  # type: ignore
ImportError: dlopen(/Users/ylk4626/miniforge3/envs/test_pxblat/lib/python3.10/site-packages/pxblat/_extc.cpython-310-darwin.so, 0
x0002): symbol not found in flat namespace '_BIO_ctrl'

Version

v1.1.1

What platform are you working on?

Mac Arm

Relevant log output

No response

Code of Conduct

• I agree to follow this project's Code of Conduct

Description

The number of clients for a server is limited to around 250 so far. Otherwise, these will be an issue:

Too many open files 
blat server may be down

note: Command Line version of BLAT does not have this issue.

INFO

• ulimit -n to control the number of open files
• it will limit the number of opening files in one python sessions.

https://github.com/cauliyang/pxblat/actions/runs/5434773166/jobs/9883431253

https://github.com/cauliyang/pxblat/pulls?q=is%3Apr+is%3Aopen+sort%3Aupdated-desc

Plan

• add a tutorial to walkthrough all features the lib provides
• provide docs for APIs (Server, Client , and free functions)

UsageStats is used to summarize the status of the Server, for example, how many files are queried to the server? what is the 2-bit file?

However, the status may be not usable when we conduct some analysis.
In other words, the user may not use the status.
Hence, I do not export to the parameter for Server.
User will not pass theUsageStats to open Server

Plan

• add the lib to bioconda
  - [ ] automate the process to bump the version and submit pr to Bioconda
• add building target of aarch64