Peptide Junction Mapper

[Chris7]

A script that converts a peptide file into a GTF/GFF file. The input for it should be a GFF/GTF file, a fasta file, and a tab delimited file.

The output:
A GFF file of mapped peptides. It should show correct splicing in IGV.

Optional output:
Statistics such as exon-exon junction counts.

Unit Tests:
Splicing
Splicing with a change in frame
Reconstruction of the input peptides from the output GFF

Here is a very hackish script which was used to make this for some human proteome data:
https://gist.github.com/Chris7/787a96beedb3b6de090c

[Chris7]

By peptide file, I mean any delimited file where the user enters the column (# or name) the peptides can be found in.