trifusion.orthomcl_pipeline module¶

trifusion.orthomcl_pipeline.adjust_fasta(file_list, dest, nm=None)[source]¶

trifusion.orthomcl_pipeline.allvsall_usearch(goodproteins, evalue, dest, cpus, usearch_outfile, usearch_bin='usearch', nm=None)[source]¶

trifusion.orthomcl_pipeline.blast_parser(usearch_ouput, dest, db_dir, nm)[source]¶

trifusion.orthomcl_pipeline.check_unique_field(proteome_file, verbose=False, nm=None)[source]¶

Checks the original proteome file for a field in the fasta header that is unique to all sequences

trifusion.orthomcl_pipeline.dump_pairs(db_dir, dest, nm=None)[source]¶

trifusion.orthomcl_pipeline.export_filtered_groups(inflation_list, group_prefix, gene_t, sp_t, sqldb, db, tmp_dir, dest, nm=None)[source]¶

trifusion.orthomcl_pipeline.filter_fasta(min_len, max_stop, db, dest, nm=None)[source]¶

trifusion.orthomcl_pipeline.install_schema(db_dir)[source]¶

Install the schema for the mySQL database

Parameters:	db_dir – string, directory for the sqlite database

trifusion.orthomcl_pipeline.main()[source]¶

trifusion.orthomcl_pipeline.mcl(inflation_list, dest, mcl_file='mcl', nm=None)[source]¶

trifusion.orthomcl_pipeline.mcl_groups(inflation_list, mcl_prefix, start_id, group_file, dest, nm=None)[source]¶

trifusion.orthomcl_pipeline.pairs(db_dir, nm=None)[source]¶

trifusion.orthomcl_pipeline.prep_fasta(proteome_file, code, unique_id, verbose=False, nm=None)[source]¶