diff mircounts.py @ 3:ee99c6374a3b draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"

--- a/mircounts.py	Tue Jul 18 06:49:21 2017 -0400
+++ b/mircounts.py	Fri Oct 18 19:18:17 2019 -0400
@@ -43,8 +43,8 @@
     """
     coverage = dict()
     for ref_name, ref_len in zip(bamfile.references, bamfile.lengths):
-        coverage[ref_name] = bamfile.count_coverage(reference=ref_name,
-                                                    start=0, end=ref_len,
+        coverage[ref_name] = bamfile.count_coverage(contig=ref_name,
+                                                    start=0, stop=ref_len,
                                                     quality_threshold=quality)
         """ Add the 4 coverage values """
         coverage[ref_name] = [sum(x) for x in
@@ -64,13 +64,13 @@
             gff_fields = line[:-1].split("\t")
             if gff_fields[2] == 'miRNA':
                 mir_name = gff_fields[0]
-                premir_name = gff_fields[8].split('=')[-1]
+                premir_name = gff_fields[8].split('Parent_mir_Name=')[-1]
                 mir_start = int(gff_fields[3])
                 mir_end = int(gff_fields[4])
                 # GFF is 1-based, pysam is 0-based.
-                counts[mir_name] = bamfile.count(reference=premir_name,
+                counts[mir_name] = bamfile.count(contig=premir_name,
                                                  start=mir_start-1,
-                                                 end=mir_end-1)
+                                                 stop=mir_end-1)
     return counts
 
 
@@ -104,7 +104,6 @@
     writes a count table
     """
     F = open(outfile, 'w')
-    F.write('Gene\tCounts\n')
     for gene in sorted(countdict):
         F.write('%s\t%s\n' % (gene, str(countdict[gene])))
     F.close()