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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
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warnings of deprecated functions biopython 1.79, but `generate` still works #211

Closed mmp3 closed 11 months ago

mmp3 commented 2 years ago

I noticed other Issues that mention that Biopython-1.79 is causing warnings and crashes.

I thought I would report that I see the same warnings, but the iss generate command still completes successfully.

In particular, the following commands completes successfully:

iss generate -n 0.25M -o test_1  --cpus 2  --mode basic  --draft genome1.fna genome2.fna genome3.fna

though it does generate a bunch of warnings:

INFO:iss.app:Starting iss generate
INFO:iss.app:Using basic ErrorModel
INFO:iss.util:Stitching input files together
INFO:iss.app:Using lognormal abundance distribution
INFO:iss.app:Using 2 cpus for read generation
INFO:iss.app:Generating 250000 reads
INFO:iss.app:Generating reads for record: GUT_GENOME000001_1
/home/ubuntu/packages/python_3.8_venv_20210618/lib/python3.8/site-packages/Bio/Seq.py:17
54: BiopythonDeprecationWarning: myseq.tomutable() is deprecated; please use MutableSeq(
myseq) instead.
  warnings.warn(
/home/ubuntu/packages/python_3.8_venv_20210618/lib/python3.8/site-packages/Bio/Seq.py:27
49: BiopythonDeprecationWarning: myseq.toseq() is deprecated; please use Seq(myseq) inst
ead.
  warnings.warn(
/home/ubuntu/packages/python_3.8_venv_20210618/lib/python3.8/site-packages/Bio/Seq.py:17
54: BiopythonDeprecationWarning: myseq.tomutable() is deprecated; please use MutableSeq(
myseq) instead.
  warnings.warn(
/home/ubuntu/packages/python_3.8_venv_20210618/lib/python3.8/site-packages/Bio/Seq.py:27
49: BiopythonDeprecationWarning: myseq.toseq() is deprecated; please use Seq(myseq) inst
ead.
  warnings.warn(
INFO:iss.app:Generating reads for record: GUT_GENOME000001_2
INFO:iss.app:Generating reads for record: GUT_GENOME000001_3
INFO:iss.app:Generating reads for record: GUT_GENOME000001_4
...

Here is some version info:

$ python3 --version
Python 3.8.10

$ pip3 show InsilicoSeq
Name: InSilicoSeq
Version: 1.5.3
Summary: a sequencing simulator
Home-page: https://github.com/HadrienG/InSilicoSeq
Author: Hadrien Gourlé
Author-email: hadrien.gourle@slu.se
License: MIT
Location: /data1/packages/python_3.8_venv_20210618/lib/python3.8/site-packages
Requires: requests, numpy, scipy, joblib, future, pysam, biopython
Required-by:

$ pip3 show Biopython
Name: biopython
Version: 1.79
Summary: Freely available tools for computational molecular biology.
Home-page: https://biopython.org/
Author: The Biopython Contributors
Author-email: biopython@biopython.org
License: UNKNOWN
Location: /data1/packages/python_3.8_venv_20210618/lib/python3.8/site-packages
Requires: numpy
Required-by: InSilicoSeq, helperlibs, antismash