Script used in the analysis of the paper "A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells".
BP-1.py is a python 2.7 BAM parser based on HTSeq that filters the alignments by their percent-identity and lenght.
BP-1.py outputs .tsv and .fasta files containing the alignments info and reads sequences respectively.
python BP-1.py <BAM_file>
Minimum alignment percent-identity and lenght can be specified by the optional arguments --min_id and --min_len.