Potentially useful Python scripts for file parsing or general purpose bioinformatics.
Reads in fasta files and non-interleaved phylip and nexus files.
Will output fasta, interleaved and non-interleaved phylip and nexus files.
Required arguments:
-i < infile >
-inf < file_type > FASTA, NEXUS or PHYLP (all caps, not misspelled).
-outf < file_type > FASTA, NEXUS or PHYLP (all caps, not misspelled).
Optional arguments:
-prot if present will write protein to nexus file. Default: DNA
-int if present will write interleaved nexus and phylip files. Default: sequential
Will find and annotate piRNA clusters from a .SAM file
Required arguments: -i < infile.sam >