# HG changeset patch
# User artbio
# Date 1504860262 14400
# Node ID 20d28cfdeefed0b8ff87d4880f431cafc5c77576
# Parent  4d9682bd3a6b71a90f2dea9ac0a531bba2a29781
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit cfdc08418887bfe4a35588cd78d0a2b6ffa6e19e

diff -r 4d9682bd3a6b -r 20d28cfdeefe overlapping_reads.py
--- a/overlapping_reads.py	Sat Sep 02 06:35:15 2017 -0400
+++ b/overlapping_reads.py	Fri Sep 08 04:44:22 2017 -0400
@@ -51,10 +51,10 @@
             for read in bam_object.fetch(chrom):
                 if not read.is_reverse:
                     all_query_positions[chrom].append(
-                        read.get_reference_positions(full_length=True)[0])
+                        read.reference_start)
                 else:
                     all_query_positions[chrom].append(
-                        read.get_reference_positions(full_length=True)[-1])
+                        read.reference_end)
             all_query_positions[chrom] = sorted(
                 list(set(all_query_positions[chrom])))
         return all_query_positions
@@ -77,42 +77,38 @@
                                                     start=pos, end=pos+overlap-1)
                 #  1
                 for queryread in iterreads_1:
-                    if queryread.get_reference_positions(
-                        full_length=True)[0] == pos and \
+                    if queryread.reference_start == pos and \
                         queryread.query_alignment_length in query_range \
                             and not queryread.is_reverse:
                         for targetread in iterreads_2:
                             if (targetread.
-                                get_reference_positions(full_length=True)[-1]
+                                get_reference_positions()[-1]
                                 == queryread.get_reference_positions(
-                                   full_length=True)[overlap-1] and
+                                   )[overlap-1] and
                                 targetread.query_alignment_length in
                                     target_range and targetread.is_reverse):
                                 targetreadseq = self.revcomp(
                                     targetread.query_sequence)
                                 stringresult.append(
                                     '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, queryread.get_reference_positions(
-                                     full_length=True)[0]+1,
+                                    (chrom, queryread.reference_start+1,
                                      'F', queryread.query_alignment_length,
                                      self.readdic[queryread.query_sequence],
                                      queryread.query_sequence))
                                 stringresult.append(
                                     '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, targetread.get_reference_positions(
-                                     full_length=True)[0]+1,
+                                    (chrom, targetread.reference_start+1,
                                      'R', targetread.query_alignment_length,
                                      self.readdic[targetread.query_sequence],
                                      targetreadseq))
                 #  2
                 for queryread in iterreads_3:
-                    if queryread.get_reference_positions(
-                        full_length=True)[-1] == pos+overlap-1 and \
+                    if queryread.reference_end-1 == pos+overlap-1 and \
                         queryread.query_alignment_length in query_range \
                             and queryread.is_reverse:
                         for targetread in iterreads_4:
                             if (targetread.
-                                get_reference_positions(full_length=True)[0]
+                                reference_start
                                 == pos and targetread.query_alignment_length
                                     in target_range and not
                                     targetread.is_reverse):
@@ -121,15 +117,13 @@
                                 targetreadseq = targetread.query_sequence
                                 stringresult.append(
                                     '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, queryread.get_reference_positions(
-                                     full_length=True)[0]+1, 'R',
+                                    (chrom, queryread.reference_start+1, 'R',
                                      queryread.query_alignment_length,
                                      self.readdic[queryread.query_sequence],
                                      queryreadseq))
                                 stringresult.append(
                                     '>%s|%s|%s|%s|n=%s\n%s\n' %
-                                    (chrom, targetread.get_reference_positions(
-                                     full_length=True)[0]+1,
+                                    (chrom, targetread.reference_start+1,
                                      'F', targetread.query_alignment_length,
                                      self.readdic[targetread.query_sequence],
                                      targetreadseq))
diff -r 4d9682bd3a6b -r 20d28cfdeefe overlapping_reads.xml
--- a/overlapping_reads.xml	Sat Sep 02 06:35:15 2017 -0400
+++ b/overlapping_reads.xml	Fri Sep 08 04:44:22 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.2">
+<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.3">
     <description />
     <requirements>
         <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>