Source code supporting Mikan et al (2018)
This GitHub git repository contains source code used for the analysis of data as part of Mikan et al (2018).
The 'java' directory contains the analysis programs for the Gene Ontology spectral counting (program/GOAnalysisProgram), comparing the spectral count ratios between samples (program/GOAnalysisProgram), and taxonomic analysis (program/TaxonomyAnalyzer).
The 'python' directory contains two scripts used in summarizing spectral counts for each peptide and determining peptide least common ancestor (LCA) taxa.
- annotate_blast_with_taxonids.py: given a file of BLAST results, associate each 'hit' UniProt protein with with its taxon according to UniProt.
- Depends on pyvalise/ext/uniprot.py to communicate with UniProt.
- infer_taxa_withblast.py: given a file with identified peptide sequences, a file mapping peptides to the proteins containing them, a set of BLAST results, and a file mapping BLAST-hit proteins to taxa, infers the LCA taxon for each peptide. This script uses the UniPept taxonomy service as a convenience for looking up the taxonomic hierarchy of each BLAST-hit taxon.
- Depends on pymeta/ncbi.py, pymeta/unipept.py and pyvalise/util/charts.py