indelPost

indelPost is a Python library for indel processing via realignment and read-based phasing to resolve alignment ambiguities. By importing the library, users write their own scripts to solve alignment-sensitive problems such as:

• compare/integrate indels that are differently called by multiple variant callers (e.g., complex indels).
• compare indel alignments in multiple mappings (e.g., match DNA indels to RNA-Seq for expression check).
• construct a complex indel from a simple indel by read-based phasing.
• extract reads supporting the target indel from BAM file.
• pull variant records matching the target indel from VCF file.
• count reads supporting indels by realignment.

Visit documentation for detail.

To install (require Linux with Python>=3.6 pre-installed):

pip3 install indelpost

or from source for develop or debug

git clone https://github.com/stjude/indelPost.git
cd indelPost 
python3 -m pip install --prefix=/home/schaudge/.local/lib/python3.10/site-packages/ --editable .  # recommand for debug mode

or

pip3 install --prefix=/home/schaudge/.local/lib/python3.10/site-packages/ --editable .

Troubleshoot

If you get something like:

... may indicate binary incompatibility. Expected 88 from C header, got 72 from PyObject

or

AttributeError: module 'pysam.libcalignmentfile' has no attribute 'IteratorColumnAll'

try:

pip3 uninstall cython pysam indelpost
pip3 install cython
pip3 install pysam
pip3 install indelpost --no-binary indelpost --no-build-isolation

Debug

Make sure the python3-dbg and cygdb were installed! And recompile the cython pyx file by python3-gdb (add gdb_debug=True parameter in cythonize!)

python3-dbg setup.py build_ext --inplace

then, begin the debug process (with source code script annotate_indels.py):

cygdb . -- --args python3-dbg annotate_indels.py

A text

Type "apropos cy" to search for commands related to "cy"...         # cy ---> cython debug command
Reading symbols from python3-dbg...
(gdb) cy break count_alleles       # function name, other format: indelpost.pileup.fetch_reads, indelpost.varaln.VariantAlignment.fetch_reads
(gdb) cy run
(gdb) cy list
(gdb) cy locals
(gdb) cy next (step)
(gdb) 

some debug tips for review:

cy break indelpost.varaln:610 # some gdb warning tips was not right! cy break indelpost.varaln.VariantAlignment.count_alleles

If "cy print variable" will be broken, try: "cy exec print(variable)" for a replacement.

Reference

Hagiwara K et al. (2022) indelPost: harmonizing ambiguities in simple and complex indel alignments. Bioinformatics

Contact

• kohei.hagiwara[AT]stjude.org