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Chris7 / pythomics

A library to assist with a variety of -omic analyses. Included are tools for proteomics, transcriptomics, and genomics.
GNU General Public License v3.0
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Peptide Junction Mapper #8

Open Chris7 opened 9 years ago

Chris7 commented 9 years ago

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 commented 9 years ago

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