def generate_params_totalRNAfunctions(): for dbname, location in P.asDict("databases").iteritems(): yield [['mappings/unique.rpkm.all', location], [ "overall_annotations/totalRNA.%s" % dbname, "overall_annotations/totalRNA_diffs.%s" % dbname ]]
def generate_fuzzy_enrich_params(): '''find enrichments.''' bad_clusters=getBadClusters() for min_rpkm, min_diff, cluster_lvl in \ itertools.product( PARAMS["min_rpkm"], PARAMS["min_diff"], PARAMS["cluster_lvl" ] ): for dbname, location in P.asDict("databases").iteritems(): if "fuzzy_k/all-%s-%s.pcl" % (min_rpkm, min_diff) in bad_clusters: continue yield [ ["fuzzy_k/background-%s-%s" % (min_rpkm, min_diff), glob.glob("fuzzy_k/cluster-%s-%s-%s.*" % (min_rpkm, min_diff, cluster_lvl)), location], ["fuzzy_k/%s-summary-cluster-%s-%s-%s.0" % (dbname, min_rpkm, min_diff, cluster_lvl), "fuzzy_k/%s-expanded-cluster-%s-%s-%s.0" % (dbname, min_rpkm, min_diff, cluster_lvl)] ]
def generate_fuzzy_enrich_params(): '''find enrichments.''' bad_clusters = getBadClusters() for min_rpkm, min_diff, cluster_lvl in \ itertools.product( PARAMS["min_rpkm"], PARAMS["min_diff"], PARAMS["cluster_lvl" ] ): for dbname, location in P.asDict("databases").iteritems(): if "fuzzy_k/all-%s-%s.pcl" % (min_rpkm, min_diff) in bad_clusters: continue yield [[ "fuzzy_k/background-%s-%s" % (min_rpkm, min_diff), glob.glob("fuzzy_k/cluster-%s-%s-%s.*" % (min_rpkm, min_diff, cluster_lvl)), location ], [ "fuzzy_k/%s-summary-cluster-%s-%s-%s.0" % (dbname, min_rpkm, min_diff, cluster_lvl), "fuzzy_k/%s-expanded-cluster-%s-%s-%s.0" % (dbname, min_rpkm, min_diff, cluster_lvl) ]]
def generate_params_totalRNAfunctions(): for dbname, location in P.asDict("databases").iteritems(): yield [['mappings/unique.rpkm.all', location], ["overall_annotations/totalRNA.%s" % dbname, "overall_annotations/totalRNA_diffs.%s" % dbname]]
def generate_params_report(): for dbname, location in P.asDict("databases").iteritems(): yield [glob.glob("fuzzy_k/%s-summary-cluster-*-*-*.*" % dbname), "best_conditions/clustering_summary_%s.txt" % dbname]
def generate_enrichments_high_expn_params(): for min_rpkm in PARAMS["min_rpkm_tree"]: for dbname, location in P.asDict("databases").iteritems(): yield [ ['mappings/unique.rpkm.all', location], "high_expn/high_expn.%s.%s" % (dbname, min_rpkm), min_rpkm ]
def generate_calculate_term_params(): for dbname, location in P.asDict("databases").iteritems(): yield [ "mappings/unique.rpkm.all", "mappings/unique.term_patterns.%s" % dbname, location ]
def generate_params_report(): for dbname, location in P.asDict("databases").iteritems(): yield [ glob.glob("fuzzy_k/%s-summary-cluster-*-*-*.*" % dbname), "best_conditions/clustering_summary_%s.txt" % dbname ]
def generate_enrichments_high_expn_params(): for min_rpkm in PARAMS["min_rpkm_tree"]: for dbname, location in P.asDict("databases").iteritems(): yield [['mappings/unique.rpkm.all', location], "high_expn/high_expn.%s.%s" % (dbname, min_rpkm), min_rpkm]