This is a collection of python scripts I've been making over the years to assist me in molecular biology and bioinformatics related work. Some were originally written in Perl, but I've since ported them to Python3. GPL-3 applies unless otherwise stated.
Sorts the ids of a FASTA file by name.
Requires argparse and biopython.
Converts an INSDSeq NCBI file to FASTA format. Has the possibility of retrieving the CDS portion of all cDNA sequences (if CDS information is available), adds "-" to correct the ORF if necessary. It also sorts the ids of a FASTA file by name.
Requires argparse and xml.etree.ElementTree.
A simple BLAST XML to FASTA converter. Adds 5' gaps to facilitate downstream alignment with query sequence.
Requires argparse and biopython.
Generates a consensus sequence from a pre-aligned FASTA file.
Requires argparse and biopython.
Converts a pDRAW32 file into FASTA.
Requires argparse and biopython.
Converts a pDRAW32 file into JSON.
Requires argparse.
Converts mispriming libraries downloaded directly from the Primer3Plus repository into Python a file that can be imported accordingly. Particularly useful for primer3-py. By default creates a file called misprime_libs.py.
Requires argparse and biopython.