Mercurial > repos > bioit_sciensano > phagetermvirome
diff _modules/generate_report.py @ 0:69e8f12c8b31 draft
"planemo upload"
| author | bioit_sciensano |
|---|---|
| date | Fri, 11 Mar 2022 15:06:20 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_modules/generate_report.py Fri Mar 11 15:06:20 2022 +0000 @@ -0,0 +1,157 @@ +from __future__ import print_function +import os +import pickle +from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Image, Table, TableStyle, PageBreak +from reportlab.lib.pagesizes import letter, landscape +from _modules.functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport + + +def loadDR(DR_path,DR): + for d in os.listdir(DR_path): # iterate over P_class subdirectories. + if not os.path.isdir(os.path.join(DR_path,d)): + err_str=DR_path+" should contain only directories." + raise RuntimeError(err_str) + for fic_name in os.listdir(os.path.join(DR_path,d)): # iterate over all files for a given P_class + p=os.path.join(DR_path,d) + fname=os.path.join(p,fic_name) + with open(fname, 'rb') as f: + loaded_items=pickle.load(f) + # d is P_class name, fic_name is phagename. + dict_tmp=dict() + dict_tmp["phagename"]=loaded_items[0] + dict_tmp["seed"]=loaded_items[1] + dict_tmp["added_whole_coverage"]=loaded_items[2] + dict_tmp["Redundant"]=loaded_items[3] + dict_tmp["P_left"]=loaded_items[4] + print("P_left=",dict_tmp["P_left"],type(dict_tmp["P_left"])) + dict_tmp["P_right"] = loaded_items[5] + print("P_right=",dict_tmp["P_right"],type(dict_tmp["P_right"])) + dict_tmp["Permuted"]=loaded_items[6] + dict_tmp["P_orient"] =loaded_items[7] + dict_tmp["termini_coverage_norm_close"] =loaded_items[8] + dict_tmp["picMaxPlus_norm_close"] =loaded_items[9] + dict_tmp["picMaxMinus_norm_close"] =loaded_items[10] + dict_tmp["gen_len"] =loaded_items[11] + dict_tmp["tot_reads"] =loaded_items[12] + dict_tmp["P_seqcoh"] =loaded_items[13] + dict_tmp["phage_plus_norm"] =loaded_items[14] + dict_tmp["phage_minus_norm"] =loaded_items[15] + dict_tmp["ArtPackmode"] = loaded_items[16] + dict_tmp["termini"] = loaded_items[17] + dict_tmp["forward"] = loaded_items[18] + dict_tmp["reverse"] = loaded_items[19] + dict_tmp["ArtOrient"] = loaded_items[20] + dict_tmp["ArtcohesiveSeq"] = loaded_items[21] + dict_tmp["termini_coverage_close"] = loaded_items[22] + dict_tmp["picMaxPlus_close"] = loaded_items[23] + dict_tmp["picMaxMinus_close"] = loaded_items[24] + dict_tmp["picOUT_norm_forw"] = loaded_items[25] + dict_tmp["picOUT_norm_rev"] = loaded_items[26] + dict_tmp["picOUT_forw"] = loaded_items[27] + dict_tmp["picOUT_rev"] = loaded_items[28] + dict_tmp["lost_perc"] = loaded_items[29] + dict_tmp["ave_whole_cov"] = loaded_items[30] + dict_tmp["R1"] = loaded_items[31] + dict_tmp["R2"] = loaded_items[32] + dict_tmp["R3"] = loaded_items[33] + dict_tmp["host"] = loaded_items[34] + dict_tmp["host_len"] = loaded_items[35] + dict_tmp["host_whole_coverage"] = loaded_items[36] + dict_tmp["picMaxPlus_host"] = loaded_items[37] + dict_tmp["picMaxMinus_host"] = loaded_items[38] + dict_tmp["surrounding"] = loaded_items[39] + dict_tmp["drop_cov"] = loaded_items[40] + dict_tmp["paired"] = loaded_items[41] + dict_tmp["insert"] = loaded_items[42] + dict_tmp["phage_hybrid_coverage"] = loaded_items[43] + dict_tmp["host_hybrid_coverage"] = loaded_items[44] + dict_tmp["added_paired_whole_coverage"] = loaded_items[45] + dict_tmp["Mu_like"] = loaded_items[46] + dict_tmp["test_run"] = loaded_items[47] + dict_tmp["P_class"] = loaded_items[48] + dict_tmp["P_type"] = loaded_items[49] + dict_tmp["P_concat"] = loaded_items[50] + dict_tmp["idx_refseq_in_list"] = loaded_items[51] + DR [d][fic_name]=dict_tmp + f.close() + + + + +def genReport(fParms,inDArgs,inRawDArgs,no_match,DR): + # Test No Match + if len(no_match) == inDArgs.nbr_virome: + print("\n\nERROR: No reads match, please check your reference file.") + exit() + + # Report Resume + multiReport = SummaryReport(inRawDArgs.phagename, DR, no_match) + multiCohSeq = "" + multiPhageSeq = "" + multiWorkflow = "#phagename\tClass\tLeft\tRight\tType\tOrient\tCoverage\tComments\n" + + # No Match in workflow + if fParms.workflow: + for no_match_contig in no_match: + multiWorkflow += WorkflowReport(no_match_contig, "-", "-", "-", "-", "-", 0, 1) + + for DPC in DR: + for DC in DR[DPC]: + # Text report + if fParms.workflow: # phagename, P_class, P_left, P_right, P_type, P_orient, ave_whole_cov, multi = 0 + multiWorkflow += WorkflowReport(DC, DR[DPC][DC]["P_class"], DR[DPC][DC]["P_left"], + DR[DPC][DC]["P_right"], + DR[DPC][DC]["P_type"], DR[DPC][DC]["P_orient"], + DR[DPC][DC]["ave_whole_cov"], 1) + + # Sequence + idx_refseq = DR[DPC][DC]["idx_refseq_in_list"] + refseq = inDArgs.refseq_liste[idx_refseq] + multiCohSeq += ExportCohesiveSeq(DC, DR[DPC][DC]["ArtcohesiveSeq"], DR[DPC][DC]["P_seqcoh"], fParms.test_run, 1) + multiPhageSeq += ExportPhageSequence(DC, DR[DPC][DC]["P_left"], DR[DPC][DC]["P_right"], refseq, + DR[DPC][DC]["P_orient"], DR[DPC][DC]["Redundant"], DR[DPC][DC]["Mu_like"], + DR[DPC][DC]["P_class"], DR[DPC][DC]["P_seqcoh"], fParms.test_run, 1) + + # Report + draw=0 # TODO VL: ask what is the use of this parameter that is alwayes 0... + multiReport = CreateReport(DC, DR[DPC][DC]["seed"], DR[DPC][DC]["added_whole_coverage"], draw, + DR[DPC][DC]["Redundant"], DR[DPC][DC]["P_left"], DR[DPC][DC]["P_right"], + DR[DPC][DC]["Permuted"], DR[DPC][DC]["P_orient"], + DR[DPC][DC]["termini_coverage_norm_close"], DR[DPC][DC]["picMaxPlus_norm_close"], + DR[DPC][DC]["picMaxMinus_norm_close"], DR[DPC][DC]["gen_len"], + DR[DPC][DC]["tot_reads"], DR[DPC][DC]["P_seqcoh"], DR[DPC][DC]["phage_plus_norm"], + DR[DPC][DC]["phage_minus_norm"], DR[DPC][DC]["ArtPackmode"], DR[DPC][DC]["termini"], + DR[DPC][DC]["forward"], DR[DPC][DC]["reverse"], DR[DPC][DC]["ArtOrient"], + DR[DPC][DC]["ArtcohesiveSeq"], DR[DPC][DC]["termini_coverage_close"], + DR[DPC][DC]["picMaxPlus_close"], DR[DPC][DC]["picMaxMinus_close"], + DR[DPC][DC]["picOUT_norm_forw"], DR[DPC][DC]["picOUT_norm_rev"], + DR[DPC][DC]["picOUT_forw"], DR[DPC][DC]["picOUT_rev"], DR[DPC][DC]["lost_perc"], + DR[DPC][DC]["ave_whole_cov"], DR[DPC][DC]["R1"], DR[DPC][DC]["R2"], + DR[DPC][DC]["R3"], DR[DPC][DC]["host"], DR[DPC][DC]["host_len"], + DR[DPC][DC]["host_whole_coverage"], DR[DPC][DC]["picMaxPlus_host"], + DR[DPC][DC]["picMaxMinus_host"], DR[DPC][DC]["surrounding"], DR[DPC][DC]["drop_cov"], + DR[DPC][DC]["paired"], DR[DPC][DC]["insert"], DR[DPC][DC]["phage_hybrid_coverage"], + DR[DPC][DC]["host_hybrid_coverage"], DR[DPC][DC]["added_paired_whole_coverage"], + DR[DPC][DC]["Mu_like"], fParms.test_run, DR[DPC][DC]["P_class"], + DR[DPC][DC]["P_type"], DR[DPC][DC]["P_concat"], 1, multiReport) + + # Workflow + if not fParms.test: + if fParms.workflow: + filoutWorkflow = open(inRawDArgs.phagename + "_workflow.txt", "w") + filoutWorkflow.write(multiWorkflow) + filoutWorkflow.close() + + # Concatene Sequences + filoutCohSeq = open(inRawDArgs.phagename + "_cohesive-sequence.fasta", "w") + filoutCohSeq.write(multiCohSeq) + filoutCohSeq.close() + + filoutPhageSeq = open(inRawDArgs.phagename + "_sequence.fasta", "w") + filoutPhageSeq.write(multiPhageSeq) + filoutPhageSeq.close() + + # Concatene Report + doc = SimpleDocTemplate("%s_PhageTerm_report.pdf" % inRawDArgs.phagename, pagesize=letter, rightMargin=10, + leftMargin=10, topMargin=5, bottomMargin=10) + doc.build(multiReport)