Merge branch 'splitreports' into 'master'

Split reports

See merge request !33

SCRIPTS/common.smk

@@ -8,14 +8,24 @@ rule copyConfig:
 		cp {input} {output}
 		"""
 
-rule buildReport:
+rule renameMainReport:
+	input:
+		report = MAINDIR+"/{project}/report-" + DEFAULT_REPORT_PART + ".html"
+	output:
+		report = MAINDIR+"/{project}/report.html"
+	shell:
+		"""
+		mv {input.report} {output.report}
+		"""
+
+rule buildReportPart:
 	input:
 		unpack(getAllFilesForReport)
 	output:
-		report = MAINDIR+"/{project}/report.html",
+		report = MAINDIR+"/{project}/report-{multipart}.html",
 	shell:
 		"""
-		python {wfbasedir}/SCRIPTS/make_html.py -c {config[conf]} -t {input.index} -p {wildcards.project} -o {output.report}
+		python {wfbasedir}/SCRIPTS/make_html.py -c {config[conf]} -t {input.index} -p {wildcards.project} -o {output.report} -m {wildcards.multipart}
 		"""
 
 rule copyTemplateFolder:

SCRIPTS/make_html.py

@@ -50,6 +50,7 @@ argParser.add_argument("-c", "--configfile", required=True, help="Jsonfile's pat
 argParser.add_argument("-t", "--templateFile", required=True, help="HTML Template's path", dest="templateFile")
 argParser.add_argument("-p", "--projectName", required=True, help="Name of the project used to select samples in config file", dest="projectName")
 argParser.add_argument("-o", "--output", required=True, help="Path of the output file", dest="output")
+argParser.add_argument("-m", "--multipart", required=True, default="main", help="Part of the multipart report", dest="multipart")
 
 def getGenomeForProject(project):
 	for s in config["samples"]:
@@ -186,7 +187,7 @@ corrFile = os.path.join(sys.path[0],"DE","corresIDorg.txt")
 # Selection of versus conditions
 conditionVS = list()
 if(project in config["comparisons"]):
-	conditionVS.extend(config["comparisons"][project]["comps"])
+	conditionVS.extend([c for c in config["comparisons"][project]["comps"] if c.get("multipart", "main") == args.multipart])
 templateVars["conditionVS"] = conditionVS
 
 templateVars["deseqres"] = dict()

SCRIPTS/make_multiplates_config.py

@@ -179,10 +179,23 @@ if (args.comparisons is not None):
     d["comparisons"][project]["performComps"] = None
     d["comparisons"][project]["comps"] = list()
 
-    for cond1,cond2 in csv.reader(args.comparisons, delimiter='\t'):
-        if(cond1!=cond2):
+
+    for row in csv.reader(args.comparisons, delimiter='\t'):
+        multipart = None
+        if len(row)==2:
+            project_comp = None
+            cond1, cond2 = row
+        else:
+            project_comp, cond1, cond2 = row
+            v = project_comp.rsplit("::", 1)
+            project_comp = v[0]
+            multipart = v[1] if len(v) > 1 else None
+        if((project_comp or project_comp == project) and cond1!=cond2):
             if(d["comparisons"][project]["performComps"]!=False):
-                d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2)]))
+                if multipart:
+                    d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2),("multipart",multipart)]))
+                else:
+                    d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2)]))
                 d["comparisons"][project]["performComps"] = True
             else:
                 eprint("ERROR make_multiplates_config.py: ","Invalid comparisons file. Both comparisons and first part secondary analysis defined.\nPlease choose if you want to perform comparisons (different conditions specified) or if you only want to perform first part of secondary analysis (identical conditions specified)")

SCRIPTS/make_srp_config.py

@@ -177,6 +177,9 @@ for sample in d["samples"]:
 d["comparisons"] = dict()
 if (args.conditions is not None):
     for project,cond1,cond2 in csv.reader(args.conditions, delimiter='\t'):
+        v = project.rsplit("::", 1)
+        project = v[0]
+        multipart = v[1] if len(v) > 1 else None
         if(not project in d["comparisons"]):
             d["comparisons"][project] = OrderedDict()
             d["comparisons"][project]["species"] = getGenomeForProject(project)
@@ -191,7 +194,10 @@ if (args.conditions is not None):
             
         if(cond1!=cond2):
             if(d["comparisons"][project]["performComps"]!=False):
-                d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2)]))
+                if multipart:
+                    d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2),("multipart",multipart)]))
+                else:
+                    d["comparisons"][project]["comps"].append(OrderedDict([("condition1",cond1),("condition2",cond2)]))
                 d["comparisons"][project]["performComps"] = True
             else:
                 eprint("ERROR make_srp_config.py: ","Invalid condition file. In project: \""+project+"\" both comparisons and first part secondary analysis defined.\nPlease choose if you want to perform comparisons (different conditions specified) or if you only want to perform first part of secondary analysis (identical conditions specified)")

Snakefile

@@ -15,6 +15,7 @@ SECONDARY_ANALYSIS_PROJECTS = {c for c in config["comparisons"] if config["compa
 NO_COMPARISONS_PROJECTS = {c for c in config["comparisons"] if not config["comparisons"][c]["performComps"]}
 DATE = str(datetime.date.today())
 TIME = str(datetime.datetime.now().strftime("%H:%M:%S"))
+DEFAULT_REPORT_PART="main"
 
 # final file outputs suffixes for primary analysis
 finalSuffixes = ["log.dat","refseq.total.dat","refseq.umi.dat","spike.total.dat","spike.umi.dat","unknown_list","well_summary.dat"]
@@ -77,11 +78,12 @@ def getAllFilesForReport(wildcards):
 		files["deseqTables"] = list()
 		files["annotation"] = list()
 		for comp in config["comparisons"][wildcards.project]["comps"]:
-			files["deseqTables"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"DEseqResFiltered.tsv"))
-			files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseGo.txt"))
-			files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseKegg.txt"))
-			files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringFunctionalEnrichment.tsv"))
-			files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringDB-genes.txt"))
+			if comp.get("multipart", DEFAULT_REPORT_PART) == wildcards.multipart:
+				files["deseqTables"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"DEseqResFiltered.tsv"))
+				files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseGo.txt"))
+				files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseKegg.txt"))
+				files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringFunctionalEnrichment.tsv"))
+				files["annotation"].append(os.path.join(MAINDIR,wildcards.project,config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringDB-genes.txt"))
 		files["index"] = os.path.join(wfbasedir,"TEMPLATE","index_SA.html")
 		
 	return files
@@ -97,7 +99,17 @@ def getTargetFiles():
 		for s in config["samples"]:
 			if(s["project"]==p):
 				targets.append(os.path.join(MAINDIR,p,config["align_folder"],s["name"]+".bai"))
-		targets.append(os.path.join(MAINDIR,p,"report.html"))
+		
+		multiparts = set()
+		for c in config["comparisons"]:
+			if (p in config["comparisons"]) and config["comparisons"][p]["performComps"]:
+				for comps in config["comparisons"][p]["comps"]:
+					multiparts.add(comps.get("multipart", DEFAULT_REPORT_PART))
+		if multiparts:
+			targets.extend([os.path.join(MAINDIR, p, "report-{}.html".format(mp)) if mp != DEFAULT_REPORT_PART else os.path.join(MAINDIR, p, "report.html") for mp in multiparts])
+		else:
+			targets.append(os.path.join(MAINDIR, p, "report.html"))
+
 		targets.append(os.path.join(MAINDIR,p,"INPUT_FILES","samplesheet_used.tsv"))
 
 	# Targets for projects with secondary analysis

multiplates.smk

@@ -10,6 +10,7 @@ wfbasedir = workflow.basedir
 MAINDIR = config["maindir"]
 DATE = str(datetime.date.today())
 TIME = str(datetime.datetime.now().strftime("%H:%M:%S"))
+DEFAULT_REPORT_PART="main"
 
 # final file outputs suffixes for primary analysis
 finalSuffixes = ["log.dat","refseq.total.dat","refseq.umi.dat","spike.total.dat","spike.umi.dat","well_summary.dat"]
@@ -53,10 +54,11 @@ def getAllFilesForReport(wildcards):
 			files["deseqTables"] = list()
 			files["annotation"] = list()
 			for comp in config["comparisons"][config["analysis_name"]]["comps"]:
-				files["deseqTables"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"DEseqResFiltered.tsv"))
-				files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseGo.txt"))
-				files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseKegg.txt"))
-				files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringFunctionalEnrichment.tsv"))
+				if comp.get("multipart", DEFAULT_REPORT_PART) == wildcards.multipart:
+					files["deseqTables"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"DEseqResFiltered.tsv"))
+					files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseGo.txt"))
+					files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"gseKegg.txt"))
+					files["annotation"].append(os.path.join(MAINDIR,config["analysis_name"],config["de_folder"],comp["condition1"]+"__vs__"+comp["condition2"],"stringFunctionalEnrichment.tsv"))
 			files["index"] = os.path.join(wfbasedir,"TEMPLATE","index_SA.html")
 
 	return files
@@ -69,9 +71,16 @@ def getTargetFiles():
 	targets.append(MAINDIR+"/"+config["analysis_name"]+"/"+config["multiqc_folder"]+"/multiqc_report.html")
 	targets.extend(expand(os.path.join(MAINDIR,config["analysis_name"],config["expression_folder"],config["analysis_name"]+".{exp}.well_summary.pdf"),exp=["unq","all"]))
 	targets.append(MAINDIR+"/config_used_in_analysis.json")
+
+	multiparts = set()
 	if(config["analysis_name"] in config["comparisons"]):
 		targets.append(MAINDIR+"/"+config["analysis_name"]+"/"+config["de_folder"]+"/exprDatUPM.tsv")
-	targets.append(MAINDIR+"/"+config["analysis_name"]+"/report.html")
+		for comps in config["comparisons"][config["analysis_name"]]["comps"]:
+			multiparts.add(comps.get("multipart", DEFAULT_REPORT_PART))
+	if multiparts:
+		targets.extend([os.path.join(MAINDIR, config["analysis_name"], "report-{}.html".format(mp)) if mp != DEFAULT_REPORT_PART else os.path.join(MAINDIR, config["analysis_name"], "report.html") for mp in multiparts])
+	else:
+		targets.append(os.path.join(MAINDIR, config["analysis_name"], "report.html".format(DEFAULT_REPORT_PART)))
 
 	return targets