--- /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)