(Work in progress!)
This is a demonstration project for CSE185. It implements a subset of the the "pileup" method available through samtools. See the samtools mpileup page for more details.
Installation requires the pyfaidx and pysam libraries to be installed. You can install these with pip:
pip install pyfaidx pysam
Once required libraries are installed, you can install mypileup with the following command:
python setup.py install
Note: if you do not have root access, you can run the commands above with additional options to install locally:
pip install --user pyfaidx pysam
python setup.py install --user
If the install was successful, typing mypileup --help should show a useful message.
The basic usage of mypileup is:
mypileup [-f ref.fasta] [other options] in.bam
To run mypileup on a small test example (using files in this repo):
mypileup -f example-files/test.fa example-files/test.bam
This should produce the output below:
chrTEST 3 C 1 ^!. F
chrTEST 4 T 2 .^!. FH
chrTEST 5 A 2 .. FH
chrTEST 6 G 2 .. FH
chrTEST 7 C 2 .. FH
chrTEST 8 T 2 .. FH
chrTEST 9 A 2 .. FH
chrTEST 10 C 2 .G FH
chrTEST 11 G 2 .. FH
chrTEST 12 T 2 .. FH
chrTEST 13 A 1 T H
To compare to output of samtools mpileup, run:
samtools mpileup --no-baq -f example-files/test.fa example-files/test.bam
The only required input to mypileup is a (sorted, indexed) BAM file. Users may additionally specify the options below:
-
-f FILE,--fasta FILE: faidx indexed reference sequence file. If specified, the mpileup format includes the reference base at each position (in column 3). Otherwise, the reference position at each base is listed as "N". -
-r REG,--region REG: region in which pileup is generated. Format chr:start-end. By default, the entire BAM file is processed. -
-o FILE,--output FILE: Write output to file. By default, output is written to stdout.
The output file format is the same as the samtools mpileup method. See: http://www.htslib.org/doc/samtools-mpileup.html
This repository was generated by Melissa Gymrek, with inspiration from the TRTools, haptools, and many other projects.
Please submit a pull request with any corrections or suggestions.
To run tests:
# Run command line tests
sh tests/cmdline_tests.sh
# Run unit tests
python -m pytest --cov=.