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View Code? Open in Web Editor NEWPython library for simple and complex indels.
Home Page: https://indelpost.readthedocs.io/en/latest/
License: Apache License 2.0
Python library for simple and complex indels.
Home Page: https://indelpost.readthedocs.io/en/latest/
License: Apache License 2.0
Hi there,
I am trying to install indelPost using:
pip install indelpost --no-binary indelpost --no-build-isolation
But have run into this error message:
error: Command "gcc -pthread -B /projects/ace_benchmarking/miniconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /projects/ace_benchmarking/miniconda3/include -fPIC -O2 -isystem /projects/ace_benchmarking/miniconda3/include -fPIC -Issw/lib/CSSWL/src -Issw/lib -I/projects/ace_benchmarking/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/projects/ace_benchmarking/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/projects/ace_benchmarking/miniconda3/include/python3.9 -c ssw/sswpy.c -o build/temp.linux-x86_64-3.9/ssw/sswpy.o -Wno-unused-function" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /projects/ace_benchmarking/miniconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-mbx157id/ssw-py_693f4359685f489a898d574632301a4b/setup.py'"'"'; __file__='"'"'/tmp/pip-install-mbx157id/ssw-py_693f4359685f489a898d574632301a4b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_i8jy1z7/install-record.txt --single-version-externally-managed --compile --install-headers /projects/ace_benchmarking/miniconda3/include/python3.9/ssw-py Check the logs for full command output.
Do you know what might be the issue?
Hi there,
I have two questions about the allele counting capabilities of indelPost that I was hoping I could get some clarity on:
Kind regards,
Fong
Hi!
i'm trying to install indelpost in order to test it for our production pipeline unfortunatly i have some issues with installation.
I'm currently working on a server with CentOS Linux release 7.7.1908, Python 3.6.13
I installed indelpost with pip:
/work/gad/shared/bin/miniconda3/bin/pip install indelpost
WARNING: Ignoring invalid distribution -yparsing (/beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages)
WARNING: Ignoring invalid distribution -yparsing (/beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages)
Requirement already satisfied: indelpost in /beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/indelpost-0.1.7-py3.6-linux-x86_64.egg (0.1.7)
Requirement already satisfied: ssw-py in /beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/ssw_py-0.2.6-py3.6-linux-x86_64.egg (from indelpost) (0.2.6)
Requirement already satisfied: numpy>=1.16.0 in /beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages (from indelpost) (1.19.5)
Requirement already satisfied: pysam>=0.15.0 in /beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages (from indelpost) (0.16.0.1)
Requirement already satisfied: cython>=0.29.12 in /beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages (from indelpost) (0.29.24)
WARNING: Ignoring invalid distribution -yparsing (/beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages)
WARNING: Ignoring invalid distribution -yparsing (/beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages)
WARNING: Ignoring invalid distribution -yparsing (/beegfs/data/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages)
pip 21.3.1
when i'm running python and tried to import indelpost lib i get this error :
from ssw_lib import CSsw
import indelpost
Traceback (most recent call last):
File "", line 1, in
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/indelpost-0.1.7-py3.6-linux-x86_64.egg/indelpost/init.py", line 1, in
from indelpost.variant import *
File "indelpost/variant.pyx", line 4, in init indelpost.variant
File "indelpost/localn.pyx", line 5, in init indelpost.localn
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/ssw/init.py", line 1, in
from . ssw_wrap import Aligner
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/ssw/ssw_wrap.py", line 259, in
class PyAlignRes(object):
File "/work/gad/shared/bin/miniconda3/lib/python3.6/site-packages/ssw/ssw_wrap.py", line 274, in PyAlignRes
cigar_int_to_len = libssw.cigar_int_to_len
File "/work/gad/shared/bin/miniconda3/lib/python3.6/ctypes/init.py", line 361, in getattr
func = self.getitem(name)
File "/work/gad/shared/bin/miniconda3/lib/python3.6/ctypes/init.py", line 366, in getitem
func = self._FuncPtr((name_or_ordinal, self))
AttributeError: /work/gad/shared/bin/Complete-Striped-Smith-Waterman-Library/src/libssw.so: undefined symbol: cigar_int_to_len
i tried to find help on the github of ssw-py, i changed my PATH, with
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/work/gad/shared/bin/Complete-Striped-Smith-Waterman-Library/src
i tried to install ssw-py with pip but it's a complete fail that's why i tried by compiling source
if you have any idea to help i would be very gratefull!
thanks !
Hi, I read your paper, this repo, and the doc at https://indelpost.readthedocs.io/en/latest/api.html and I still do not know how to construct a complex indel from simple variants. For example, from a VCF file generated by Mutect/Strelka/UVC as input, how do I get a new VCF file with small variants fused into complex indels.
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