update gtf prepare

LuChenLab · Mar 11, 2022 · f124bea · f124bea
1 parent 8086280
commit f124bea
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/cli/prepare.py b/cli/prepare.py
@@ -136,11 +136,13 @@ def prepare(
     sort and merge utr region information
     """
     bedtmp = pybedtools.BedTool(utr_outfile)
-    bedtmp = bedtmp.sort().merge(d=500, s = True, o='distinct', c='6')
-    mt_tmp = pybedtools.BedTool('\n'.join(mt_lst), from_string=True).sort().merge(s=True, o='distinct', c='6')
+    bedtmp = bedtmp.sort().merge(d=500, s = True)
+
     utr_out = open(utr_outfile, 'w')
     utr_out.write(str(bedtmp))
-    utr_out.write(str(mt_tmp))
+    if mt_lst:
+        mt_tmp = pybedtools.BedTool('\n'.join(mt_lst), from_string=True).sort().merge(s=True)
+        utr_out.write(str(mt_tmp))
     utr_out.close()
 
     """
@@ -152,7 +154,7 @@ def prepare(
         '\n'.join(intron_lst), 
         from_string=True
         )
-    intron_bed = intron_bed.sort().merge(s = True, o='distinct', c='6')
+    intron_bed = intron_bed.sort().merge(s = True)
     intron_bed = intron_bed.intersect(bedtmp, v=True)
     intron_lst = []
     for line in intron_bed:

diff --git a/utils/isoform.py b/utils/isoform.py
@@ -40,8 +40,8 @@ def structure(self):
 
                 if "transcript_biotype" in line.attributes:
                     gene_structure[gid][tid]["transcript_biotype"] = line.attributes["transcript_biotype"]
-                elif "transcript_biotype" in line.attributes:
-                    gene_structure[gid][tid]["transcript_biotype"] = line.attributes["transcript_biotype"]
+                elif "transcript_type" in line.attributes:
+                    gene_structure[gid][tid]["transcript_type"] = line.attributes["transcript_type"]
 
                 gene_structure[gid][tid]["strand"] = line.strand
                 gene_structure[gid][tid][line.feature].append(