diff --git a/_modules/functions_PhageTerm.py b/_modules/functions_PhageTerm.py index 63db8b31c46153491da95b91c6a9698b8e8c6536..f158300788bbfe1f7635860d5f7cd1f46595282e 100644 --- a/_modules/functions_PhageTerm.py +++ b/_modules/functions_PhageTerm.py @@ -340,7 +340,7 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta print("WARNING: No read Match, please check your fastq file") termini_coverage = correctEdge(termini_coverage, fParms.edge) - #paired_whole_coverage = correctEdge(whole_coverage, fParms.edge) #TODO: discuss with Julian and Max about the PE issue that Max reported. + paired_whole_coverage = correctEdge(whole_coverage, fParms.edge) #TODO: discuss with Julian and Max about the PE issue that Max reported. whole_coverage = correctEdge(whole_coverage, fParms.edge) phage_hybrid_coverage = correctEdge(phage_hybrid_coverage, fParms.edge) if inDArgs.hostseq != "": @@ -694,19 +694,15 @@ def ExportStatistics(phagename, whole_coverage, paired_whole_coverage, termini_c export = pd.DataFrame() # ORGANIZE Column export["Position"] = list(phage_plus_norm.sort_values("Position")["Position"]) - if paired != "": - export["Coverage +"] = paired_whole_coverage[0] - else: - export["Coverage +"] = whole_coverage[0] + # coverage values for whole_coverage == paired_whole_coverage in the single-end case + export["Coverage +"] = paired_whole_coverage[0] export["SPC +"] = termini_coverage[0] export["T +"] = [format(x/100.0,'0.2') for x in list(phage_plus_norm.sort_values("Position")["SPC_std"])] export["T + (close)"] = [format(x/100.0,'0.2') for x in list(phage_plus_norm.sort_values("Position")["SPC"])] export["pvalue +"] = [format(x,'0.2e') for x in list(phage_plus_norm.sort_values("Position")["pval_gamma"])] export["padj +"] = [format(x,'0.2e') for x in list(phage_plus_norm.sort_values("Position")["pval_gamma_adj"])] - if paired != "": - export["Coverage -"] = whole_coverage[1] - else: - export["Coverage -"] = paired_whole_coverage[1] + # coverage values for whole_coverage == paired_whole_coverage in the single-end case + export["Coverage -"] = paired_whole_coverage[1] export["SPC -"] = termini_coverage[1] export["T -"] = [format(x/100.0,'0.2') for x in list(phage_minus_norm.sort_values("Position")["SPC_std"])] export["T - (close)"] = [format(x/100.0,'0.2') for x in list(phage_minus_norm.sort_values("Position")["SPC"])]