Command line program to generate WIG tracks (sequence coverage, physical coverage, average insert length, ...) from a SAM/BAM file.
Academic project for the Bioinformatics course at University of Padova. Written in Python 3 using PySAM.
- Check to have a Python 3 interpreter
python3 --version - Install PySAM
pip3 install pysam - Generate the sequence coverage
./gtrack.py sequence_coverage -g genome.fasta -i alignments.sam -o sequence_coverage.wig
./gtrack.py sequence_coverage -g genome.fasta -i alignments.sam -o sequence_coverage.wig
./gtrack.py sequence_coverage -l 123456789000 -i alignments.sam -o sequence_coverage.wig
./gtrack.py physical_coverage -g genome.fasta -i alignments.sam > physical_coverage.wig
./gtrack.py physical_coverage -g genome.fasta -i alignments.sam -o physical_coverage.wig
./gtrack.py average_insert -g genome.fasta -i alignments.sam -o physical_coverage.wig
./gtrack.py average_insert --min 100 --max 50000 -g genome.fasta -i alignments.sam -o physical_coverage.wig
...
usage: gtrack.py [-h] -i INPUT [-o OUTPUT] (-l LENGTH | -g GENOME) [--min MIN]
[--max MAX]
{sequence_coverage,rf_mates,hs_cigar,average_insert,ff_mates,fr_mates,single_mate,rr_mates,ffrr_mates,multiple_mapping,physical_coverage_lowmem,sequence_coverage_lowmem,physical_coverage}
Generate WIG tracks from reads aligned on a reference genome.
positional arguments:
{sequence_coverage,rf_mates,hs_cigar,average_insert,ff_mates,fr_mates,single_mate,rr_mates,ffrr_mates,multiple_mapping,physical_coverage_lowmem,sequence_coverage_lowmem,physical_coverage}
Name of the track to be computed.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
SAM/BAM input file.
-o OUTPUT, --output OUTPUT
WIG output file. The default is stdout.
-l LENGTH, --length LENGTH
Length of the reference genome.
-g GENOME, --genome GENOME
Fasta file of the reference genome.
--min MIN Inserts below this value will be ignored.
--max MAX Inserts above this value will be ignored.
Genome-track generates WIG tracks from reads aligned on a reference genome.
Copyright (C) 2016 Federico Poli federpoli@gmail.com
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.