Prepare for fmt for grouped and fmt for ungrouped.

tanghaibao · Jul 17, 2018 · 36e3d8d · 36e3d8d
1 parent 462618c
commit 36e3d8d
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Showing 2 changed files with 26 additions and 4 deletions.
diff --git a/goatools/grouper/aart_geneproducts_all.py b/goatools/grouper/aart_geneproducts_all.py
@@ -40,7 +40,11 @@ def __init__(self, grprdflt, hdrobj, **kws):
     def run(self, name, goea_nts, log):
         """Run gene product ASCII art."""
         objaart = AArtGeneProductSetsOne(name, goea_nts, self)
-        return objaart.prt_report(log)
+        if self.hdrobj.sections:
+            return objaart.prt_report_grp1(log)
+        else:
+            return objaart.prt_report_grp0(log)
+
 
     def prt_mrks(self, name_marks_list, prt=sys.stdout):
         """Print summary of all GOEAs.

diff --git a/goatools/grouper/aart_geneproducts_one.py b/goatools/grouper/aart_geneproducts_one.py
@@ -31,13 +31,31 @@ def __init__(self, name, goea_results, obj):
         self.gene2section2gos = _ini.get_gene2section2gos(self.gene2gos, self.sec2gos)
         self.gene2aart = _ini.get_gene2aart(self.gene2section2gos, self.sec2chr)
 
-    def prt_report(self, prt=sys.stdout, **kws_grp):
-        """Print full GO/gene report."""
+    def prt_report_grp0(self, prt=sys.stdout):
+        """Print full GO/gene report without grouping."""
+        summaryline = self.str_summaryline()
+        kws_grp = {'use_sections':False,
+                   'hdrgo_prt':False,
+                   'sortby':lambda nt: [-1*nt.dcnt, nt.depth]}
+        # Print grouped GO IDs
+        prt.write("{SUMMARY}\n".format(SUMMARY=summaryline))
+        self.prt_gos_grouped(sys.stdout, **kws_grp)
+        # genes
+        genes = sorted(self.gene2gos.keys())
+        prt.write("\n\n{SUMMARY}\n\n".format(SUMMARY=summaryline))
+        self.prt_gene_aart(genes, prt)
+        # Sort genes
+        prt.write("\n\n{SUMMARY}\n\n".format(SUMMARY=summaryline))
+        self.prt_gene_aart_details(genes, prt)
+        return (self.name, self.get_section_marks())
+
+    def prt_report_grp1(self, prt=sys.stdout, **kws_grp):
+        """Print full GO/gene report with grouping."""
         summaryline = self.str_summaryline()
         # Print grouped GO IDs
         prt.write("{SUMMARY}\n".format(SUMMARY=summaryline))
         self.prt_gos_grouped(prt, **kws_grp)
-        # Clustered genes
+        # genes
         genes = sorted(self.gene2gos.keys())
         prt.write("\n\n{SUMMARY}\n\n".format(SUMMARY=summaryline))
         self.prt_section_key(prt)