readcomb 0.0.2

Fast detection of recombinant reads in BAMs

Readcomb - fast detection of recombinant reads in BAMs

What is it?

Readcomb is a hybrid command line script and Python module for the filtering and classification of bam sequences based on their phase change properties.

Installation

pip install readcomb

Dependencies

• cyvcf2 - Fast retrieval and filtering of vcf files and vcf objects written in C
• pysam - Interface for SAM and BAM files and provides SAM and BAM objects
• pandas - Support for data tables
• tqdm - Provides updating progress bars for command line programs
• samtools

Usage:

bamprep

Command line preprocessing script for bam files

Optional parameters:

vcfprep

Command line preprocessing script for vcf files

readcomb-vcfprep --vcf [vcf_filepath] --out [output_filepath]

Optional arguments

• --snps_only, Keep only SNPs
• --indels_only, Keep only indels
• --no_hets, Remove heterozygote calls
• --min_GQ [quality], Minimum genotype quality at both sites (default is 30)

filter

Command line multiprocessing script for identification of bam sequences with phase changes

readcomb-filter --bam [bam_filepath] --vcf [vcf_filepath]

Optional arguments:

• -p, --processes [processes], Number of processes available for filter (default is 4)
• -m, --mode [phase_change|no_match], Filtering mode (default phase_change)
• -l, --log [log_filepath], Filename for log metric output
• -o, --out [output_filepath], File to write filtered output to (default recomb_diagnosis)

classification

Python module for detailed classification of sequences containing phase changes

from readcomb.classification import rc

# generate list of bam read pairs
pairs = rc.pairs_creation(bam_filepath, vcf_filepath)

# call each of the pairs to analyse and classify them
# map and lambda function
map(lambda x:x.call(), pairs)

# or use a for loop
for pair in pairs:
    pair.call() 

# get classification of first read pair
pairs[0].classify
# > gene_conversion

License

GNU General Public License v3 (GPLv3+)

Development

Currently in alpha

Source code

Development repo