stjude / indelpost Goto Github PK

Hi there,

I have two questions about the allele counting capabilities of indelPost that I was hoping I could get some clarity on:

1. Is there a specific indel length that indelPost struggles to accurately calculate allele counts for? For instance, would you expect indelPost to perform well at say an indel length of 51 for reads that are 150 base pairs long?
2. While indelPost is designed for indel, is it possible to use its allele counting capabilities for SNVs and MNVs?

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 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, 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.