Running and Verifying Pysam

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the pysam-0.15.4/tests/pysam_data/ folder in the Pysam source code directory and locate example_aligned_pairs.sam.

   cd tests/pysam_data/

3. Run Pysam.

   python3
   import pysam
   samfile = pysam.AlignmentFile("example_aligned_pairs.sam")
   samfile.count()

   In the command output, 52 indicates that the Pysam has successfully parsed the sam file.