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).
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.
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.
The logic is based ont the psl2sam.pl script in the rackj package, which in turn is based on the converter in samtools.
- 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
XSflag is currently not set.