# HG changeset patch
# User peterjc
# Date 1495189150 14400
# Node ID cc86a2b3dc8e88649c9a14cc3bef62dfb320b718
# Parent  7a05cb080ea5b4df5c271330b1f28907611806ad
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 7138d537aaec46596985acf123348fe6f99cd6f1-dirty

diff -r 7a05cb080ea5 -r cc86a2b3dc8e tools/count_roi_variants/count_roi_variants.py
--- a/tools/count_roi_variants/count_roi_variants.py	Thu May 11 12:43:27 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.py	Fri May 19 06:19:10 2017 -0400
@@ -37,7 +37,8 @@
 AGCCCATGAGATGGGAAGCAATGGGCTACA	14	87.50
 AGCCCATGAGATGGGAAGCAATGGGCTACG	1	6.25
 AGCGCATGAGATGGGAAGCAATGGGCTACG	1	6.25
-"""
+"""  # noqa: E501
+
 if len(sys.argv) == 5:
     bam_filename, bai_filename, tabular_filename, region = sys.argv[1:]
 else:
@@ -142,31 +143,41 @@
             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("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')]
 
 
 def get_roi(seq, cigar_ops, start, end):