/bioinfo-alignment-project

bioinfo-alignment-project: a college project at unimib

Primary LanguagePython

bioinfo-alignment-project

Program to print reads from a SAM/BAM file filtered for start positions.

$ python app.py -h
usage: app.py [-h] -f FILE [-p POS [POS ...]]

Print reads from a SAM/BAM file filtered for start positions.

optional arguments:
  -h, --help                              show this help message and exit
  -f FILE, --file FILE                    path to input file
  -p POS [POS ...], --pos POS [POS ...]   list of positions
W/ Docker
docker build -t bioinfo-alignment-project .

docker run \
  -v /host/path/to/examples/:/usr/src/app/examples/ \
  bioinfo-alignment-project \
  [-h] -f FILE [-p POS [POS ...]]

Dependencies

Debian / Ubuntu
sudo apt-get install libbz2-dev liblzma-dev python3-dev samtools

sudo -H python3 -m pip install pysam