Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (Li 2009), such as those routinely created by next-generation sequencing methods.
Pysam is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Installation:
$ git clone https://github.com/Munchic/pysam/ $ cd pysam $ python setup.py install --user
Usage (adapted from https://samtools.github.io/bcftools/bgzf-aes-encryption.pdf):
# Generate a random private key and its hash (digest)
$ KEY=`dd if=/dev/urandom bs=1 count=32 2>/dev/null | xxd -ps -c32`
$ HASH=`echo $KEY | openssl sha256 | cut -f2 -d ' '`
$ echo -e "$HASH\t$KEY" > hts-keys.txt
# Configure environment variables, compress + encrypt, and index with built-in crypto htslib
$ export HTS_KEYS=hts-keys.txt
$ HTS_ENC=${PRIVATE_KEY} htslib/bgzip -c in.vcf > enc.vcf.gz
$ HTS_ENC=${PRIVATE_KEY} htslib/tabix enc.vcf.gz
# Read encrypted tabix-indexed file in Python with Pysam
import pysam
file = pysam.TabixFile("enc.vcf.gz")
for read in file.fetch('chr1'):
print(read)
The latest version is available through pypi. To install, simply type:
pip install pysam
If you are using the conda packaging manager (e.g. miniconda or anaconda), you can install pysam from the bioconda channel:
conda config --add channels r
conda config --add channels bioconda
conda install pysam
Pysam documentation is available through https://readthedocs.org/ from here
Questions and comments are very welcome and should be sent to the pysam user group