Mercurial > repos > artbio > mircounts

diff mircounts.py @ 13:b045c30fb768 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"
author artbio
date Fri, 18 Oct 2019 19:18:50 -0400
parents 2a08a6eb471c
children
line wrap: on
line diff
--- a/mircounts.py	Sat May 12 09:06:24 2018 -0400
+++ b/mircounts.py	Fri Oct 18 19:18:50 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
@@ -68,9 +68,9 @@
                 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