Uncle PSL: a BLAT to SAM converter

The package performs conversion of BLAT output (PSL) to SAM format. If the -N option is used then deletions larger than the specified limit are represented by the N CIGAR operation.

Conversion was tested on simulated reads against output generated by bwa mem (under the uncle_PSL/test/data directory).

Installation

Quick install using pip:

pip install git+https://github.com/bsipos/uncle_psl.git

Or clone the package:

git clone https://github.com/bsipos/uncle_psl.git

Install the package:

python setup.py install

Install the package in developer mode:

python setup.py develop

Run the tests:

make test

Build the documentation:

make docs

Issue make help to get a list of make targets.

Documentation

usage: uncle_psl.py [-h] [-f reads_fasta] [-N n_limit] [-H] [infile] [outfile]

Script to convert PSL files (BLAT output) to SAM format.

positional arguments:
  infile          Input PSL (default: stdin).
  outfile         Output SAM (default: stdout)

optional arguments:
  -h, --help      show this help message and exit
  -f reads_fasta  Reads in fasta format.
  -N n_limit      Use N CIGAR operation for deletions larger than this
                  parameter (None).
  -H              Use hard clipping instead of soft clipping.

Credits

The logic is based ont the psl2sam.pl script in the rackj package, which in turn is based on the converter in samtools.

Limitations

• SAM header is not written, but that can be easily added using samtools view -T
• The MD flag is not added, but that can be easily done using samtools calmd.
• Mapping qualities are set to zero.
• Base qualities are not added to the SAM output.
• The XS flag is currently not set.