# HG changeset patch
# User peterjc
# Date 1494940458 14400
# Node ID 3ee6f4d0ac80426851bc81e4144c9817c6c46311
# Parent  95efbdb729615513c1db0e6fef9da8276e72f35c
v0.0.5 Fix version inconsistency, using samtools v1.2 now.

diff -r 95efbdb72961 -r 3ee6f4d0ac80 tools/count_roi_variants/README.rst
--- a/tools/count_roi_variants/README.rst	Wed Feb 01 07:10:26 2017 -0500
+++ b/tools/count_roi_variants/README.rst	Tue May 16 09:14:18 2017 -0400
@@ -80,6 +80,9 @@
 v0.0.2  - Cope with pipes in reference name (e.g. NCBI style FASTA naming)
 v0.0.3  - Include a functional test for using an unrecognised reference.
 v0.0.4  - Improved usage text and README for use outside of Galaxy.
+v0.0.5  - Fix samtools dependency version inconsistency, using v1.2 now.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
@@ -93,17 +96,17 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/count_roi_variants/
+    $ planemo shed_update -t testtoolshed --check_diff tools/count_roi_variants/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/count_roi_variants/
+    $ planemo shed_update -t toolshed --check_diff tools/count_roi_variants/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/count_roi_variants/
+    $ planemo shed_upload --tar_only tools/count_roi_variants/
     ...
     $ tar -tzf shed_upload.tar.gz
     tools/count_roi_variants/README.rst
diff -r 95efbdb72961 -r 3ee6f4d0ac80 tools/count_roi_variants/count_roi_variants.py
--- a/tools/count_roi_variants/count_roi_variants.py	Wed Feb 01 07:10:26 2017 -0500
+++ b/tools/count_roi_variants/count_roi_variants.py	Tue May 16 09:14:18 2017 -0400
@@ -12,9 +12,10 @@
 the observed variants spanning the ROI, and outputs this as a
 tabular file.
 """
-import sys
+
 import os
 import subprocess
+import sys
 import tempfile
 
 if "-v" in sys.argv or "--version" in sys.argv:
@@ -97,7 +98,9 @@
     return answer
 
 
-assert decode_cigar("14S15M1P1D3P54M1D34M5S") == [(14, 'S'), (15, 'M'), (1, 'P'), (1, 'D'), (3, 'P'), (54, 'M'), (1, 'D'), (34, 'M'), (5, 'S')]
+assert decode_cigar("14S15M1P1D3P54M1D34M5S") == [(14, 'S'), (15, 'M'), (1, 'P'),
+                                                  (1, 'D'), (3, 'P'), (54, 'M'),
+                                                  (1, 'D'), (34, 'M'), (5, 'S')]
 
 
 def align_len(cigar_ops):
@@ -138,16 +141,32 @@
         else:
             raise NotImplementedError("Unexpected CIGAR operator %s" % op)
 
+
 assert list(expand_cigar("ACGT", decode_cigar("4M"))) == [(0, "A"), (1, "C"), (2, "G"), (3, "T")]
 assert list(expand_cigar("ACGT", decode_cigar("2=1X1="))) == [(0, "A"), (1, "C"), (2, "G"), (3, "T")]
 assert list(expand_cigar("ACGT", decode_cigar("2M1D2M"))) == [(0, "A"), (1, "C"), (3, "G"), (4, "T")]
 assert list(expand_cigar("ACtGT", decode_cigar("2M1I2M"))) == [(0, "A"), (1, "C"), (1.5, "t"), (2, "G"), (3, "T")]
 assert list(expand_cigar("tACGT", decode_cigar("1I4M"))) == [(-0.5, 't'), (0, 'A'), (1, 'C'), (2, 'G'), (3, 'T')]
 assert list(expand_cigar("ACGTt", decode_cigar("4M1I"))) == [(0, 'A'), (1, 'C'), (2, 'G'), (3, 'T'), (3.5, 't')]
-assert list(expand_cigar("AAAAGGGGTTTT", decode_cigar("12M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), (3, 'A'), (4, 'G'), (5, 'G'), (6, 'G'), (7, 'G'), (8, 'T'), (9, 'T'), (10, 'T'), (11, 'T')]
-assert list(expand_cigar("AAAAcGGGGTTTT", decode_cigar("4M1I8M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), (3, 'A'), (3.5, 'c'), (4, 'G'), (5, 'G'), (6, 'G'), (7, 'G'), (8, 'T'), (9, 'T'), (10, 'T'), (11, 'T')]
-assert list(expand_cigar("AAAAGGGGcTTTT", decode_cigar("8M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), (3, 'A'), (4, 'G'), (5, 'G'), (6, 'G'), (7, 'G'), (7.5, "c"), (8, 'T'), (9, 'T'), (10, 'T'), (11, 'T')]
-assert list(expand_cigar("AAAAcGGGGcTTTT", decode_cigar("4M1I4M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'), (3, 'A'), (3.5, 'c'), (4, 'G'), (5, 'G'), (6, 'G'), (7, 'G'), (7.5, 'c'), (8, 'T'), (9, 'T'), (10, 'T'), (11, 'T')]
+assert list(expand_cigar("AAAAGGGGTTTT", decode_cigar("12M"))) == [(0, 'A'), (1, 'A'), (2, 'A'),
+                                                                   (3, 'A'), (4, 'G'), (5, 'G'),
+                                                                   (6, 'G'), (7, 'G'), (8, 'T'),
+                                                                   (9, 'T'), (10, 'T'), (11, 'T')]
+assert list(expand_cigar("AAAAcGGGGTTTT", decode_cigar("4M1I8M"))) == [(0, 'A'), (1, 'A'), (2, 'A'),
+                                                                       (3, 'A'), (3.5, 'c'), (4, 'G'),
+                                                                       (5, 'G'), (6, 'G'), (7, 'G'),
+                                                                       (8, 'T'), (9, 'T'), (10, 'T'),
+                                                                       (11, 'T')]
+assert list(expand_cigar("AAAAGGGGcTTTT", decode_cigar("8M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'),
+                                                                       (3, 'A'), (4, 'G'), (5, 'G'),
+                                                                       (6, 'G'), (7, 'G'), (7.5, "c"),
+                                                                       (8, 'T'), (9, 'T'), (10, 'T'),
+                                                                       (11, 'T')]
+assert list(expand_cigar("AAAAcGGGGcTTTT", decode_cigar("4M1I4M1I4M"))) == [(0, 'A'), (1, 'A'), (2, 'A'),
+                                                                            (3, 'A'), (3.5, 'c'), (4, 'G'),
+                                                                            (5, 'G'), (6, 'G'), (7, 'G'),
+                                                                            (7.5, 'c'), (8, 'T'), (9, 'T'),
+                                                                            (10, 'T'), (11, 'T')]
 
 
 def get_roi(seq, cigar_ops, start, end):
@@ -167,6 +186,7 @@
     # want to exclude e.g. 3.5 and 7.5 when given start 4 and end 8.
     return "".join(base for i, base in expand_cigar(seq, cigar_ops) if start <= i <= end - 1)
 
+
 assert "GGGG" == get_roi("AAAAGGGGTTTT", decode_cigar("12M"), 4, 8)
 assert "GGGG" == get_roi("AAAAcGGGGTTTT", decode_cigar("4M1I8M"), 4, 8)
 assert "GGGG" == get_roi("AAAAGGGGcTTTT", decode_cigar("8M1I4M"), 4, 8)
@@ -176,6 +196,10 @@
 
 
 def count_region():
+    """Count reads mapped to the region.
+
+    Calls samtools view and parses the output.
+    """
     # Could recreate the region string (with no commas in start/end)?
     # region = "%s:%i-%i" % (ref, start, end)
 
@@ -211,13 +235,15 @@
     if return_code:
         sys.exit("Got return code %i from samtools view" % return_code)
     elif "specifies an unknown reference name. Continue anyway." in stderr:
-        sys.exit(stderr.strip() + "\n\nERROR: samtools did not recognise the region requested, can't count any variants.")
+        sys.exit(stderr.strip() +
+                 "\n\nERROR: samtools did not recognise the region requested, "
+                 "can't count any variants.")
 
     return tally
 
 
 def record_counts():
-
+    """Record counts to tabular file."""
     tally = count_region()
     total = sum(tally.values())
 
diff -r 95efbdb72961 -r 3ee6f4d0ac80 tools/count_roi_variants/count_roi_variants.xml
--- a/tools/count_roi_variants/count_roi_variants.xml	Wed Feb 01 07:10:26 2017 -0500
+++ b/tools/count_roi_variants/count_roi_variants.xml	Tue May 16 09:14:18 2017 -0400
@@ -1,16 +1,14 @@
-<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.3">
+<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.5">
     <description>using samtools view</description>
     <requirements>
-        <requirement type="binary">samtools</requirement>
-        <requirement type="package" version="1.2.2">samtools</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">count_roi_variants.py --version</version_command>
-    <command interpreter="python">count_roi_variants.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular" "$region"</command>
+    <version_command>
+python $__tool_directory__/count_roi_variants.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/count_roi_variants.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' '$region'
+    </command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Input BAM file" />
         <param name="region" type="text" label="Region of interest" help="Use the reference:start-end syntax as in samtools.">