Mercurial > repos > mheinzl > variant_analyzer2

changeset 83:8cec772c0bf1 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author mheinzl
date Fri, 05 Aug 2022 08:23:34 +0000
parents c2e8932b4d8d
children e46d5e377760
files read2mut.py test-data/Variant_Analyzer_allele_frequencies_test.xlsx test-data/Variant_Analyzer_summary_test.csv test-data/Variant_Analyzer_summary_test.xlsx test-data/Variant_Analyzer_tiers_test.xlsx
diffstat 5 files changed, 34 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/read2mut.py	Wed Jul 27 08:59:00 2022 +0000
+++ b/read2mut.py	Fri Aug 05 08:23:34 2022 +0000
@@ -1525,81 +1525,81 @@
                          ("Tier 5.5", "variant is close to softclipping in one of the SSCS (no information of the second mate)"),
                          ("Tier 6", "mates with contradictory information"),
                          ("Tier 7", "remaining variants")]
-    examples_tiers = [[("chr5-11068-C-G", "1.1", "AAAAAGATGCCGACTACCTT", "ab1.ba2", "254", "228", "287", "288", "289",
+    examples_tiers = [[("chr5-11068-C-G", "1.1", "alt", "AAAAAGATGCCGACTACCTT", "ab1.ba2", "254", "228", "287", "288", "289",
                         "3", "6", "3", "6", "0", "0", "3", "6", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0",
                         "4081", "4098", "5", "10", "", ""),
-                       ("", "", "AAAAAGATGCCGACTACCTT", "ab2.ba1", None, None, None, None,
+                       ("", "", "", "AAAAAGATGCCGACTACCTT", "ab2.ba1", None, None, None, None,
                         "289", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None,
                         "0", "0", "0", "0", "0", "0", "4081", "4098", "5", "10", "", "")],
-                      [("chr5-11068-C-G", "1.1", "AAAAATGCGTAGAAATATGC", "ab1.ba2", "254", "228", "287", "288", "289",
+                      [("chr5-11068-C-G", "1.1", "alt", "AAAAATGCGTAGAAATATGC", "ab1.ba2", "254", "228", "287", "288", "289",
                         "33", "43", "33", "43", "0", "0", "33", "43", "0", "0", "1", "1", "0", "0", "0", "0", "0",
                         "0", "4081", "4098", "5", "10", "", ""),
-                       ("", "", "AAAAATGCGTAGAAATATGC", "ab2.ba1", "268", "268", "270", "288", "289",
+                       ("", "", "", "AAAAATGCGTAGAAATATGC", "ab2.ba1", "268", "268", "270", "288", "289",
                         "11", "34", "10", "27", "0", "0", "10", "27", "0", "0", "1", "1", "0", "0", "1",
                         "7", "0", "0", "4081", "4098", "5", "10", "", "")],
-                      [("chr5-10776-G-T", "1.2", "CTATGACCCGTGAGCCCATG", "ab1.ba2", "132", "132", "287", "288", "290",
+                      [("chr5-10776-G-T", "1.2", "alt", "CTATGACCCGTGAGCCCATG", "ab1.ba2", "132", "132", "287", "288", "290",
                         "4", "1", "4", "1", "0", "0", "4", "1", "0", "0", "1", "1", "0", "0", "0", "0",
                         "0", "0", "1", "6", "47170", "41149", "", ""),
-                       ("", "", "CTATGACCCGTGAGCCCATG", "ab2.ba1", "77", "132", "233", "200", "290",
+                       ("", "", "", "CTATGACCCGTGAGCCCATG", "ab2.ba1", "77", "132", "233", "200", "290",
                         "4", "1", "4", "1", "0", "0", "4", "1", "0", "0", "1", "1", "0", "0", "0", "0",
                         "0", "0", "1", "6", "47170", "41149", "", "")],
-                      [("chr5-11068-C-G", "2.1", "AAAAAAACATCATACACCCA", "ab1.ba2", "246", "244", "287", "288", "289",
+                      [("chr5-11068-C-G", "2.1", "alt", "AAAAAAACATCATACACCCA", "ab1.ba2", "246", "244", "287", "288", "289",
                         "2", "8", "2", "8", "0", "0", "2", "8", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0",
                         "4081", "4098", "5", "10", "", ""),
-                       ("", "", "AAAAAAACATCATACACCCA", "ab2.ba1", None, None, None, None,
+                       ("", "", "", "AAAAAAACATCATACACCCA", "ab2.ba1", None, None, None, None,
                         "289", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0", "0",
                         "0", "0", "0", "0", "4081", "4098", "5", "10", "", "")],
-                      [("chr5-11068-C-G", "2.2", "ATCAGCCATGGCTATTATTG", "ab1.ba2", "72", "72", "217", "288", "289",
+                      [("chr5-11068-C-G", "2.2", "alt", "ATCAGCCATGGCTATTATTG", "ab1.ba2", "72", "72", "217", "288", "289",
                         "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0",
                         "4081", "4098", "5", "10", "", ""),
-                       ("", "", "ATCAGCCATGGCTATTATTG", "ab2.ba1", "153", "164", "217", "260", "289",
+                       ("", "", "", "ATCAGCCATGGCTATTATTG", "ab2.ba1", "153", "164", "217", "260", "289",
                         "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0",
                         "4081", "4098", "5", "10", "", "")],
-                      [("chr5-11068-C-G", "2.3", "ATCAATATGGCCTCGCCACG", "ab1.ba2", None, None, None, None,
+                      [("chr5-11068-C-G", "2.3", "alt", "ATCAATATGGCCTCGCCACG", "ab1.ba2", None, None, None, None,
                         "289", "0", "5", "0", "5", "0", "0", "0", "5", None, None, None, "1", "0",
                         "0", "0", "0", "0", "0", "4081", "4098", "5", "10", "", ""),
-                       ("", "", "ATCAATATGGCCTCGCCACG", "ab2.ba1", "202", "255", "277", "290", "289",
+                       ("", "", "", "ATCAATATGGCCTCGCCACG", "ab2.ba1", "202", "255", "277", "290", "289",
                         "1", "3", "1", "3", "0", "0", "1", "3", "0", "0", "1", "1", "0", "0", "0", "0",
                         "0", "0", "4081", "4098", "5", "10", "", "")],
-                      [("chr5-11068-C-G", "2.4", "ATCAGCCATGGCTATTTTTT", "ab1.ba2", "72", "72", "217", "288", "289",
+                      [("chr5-11068-C-G", "2.4", "alt", "ATCAGCCATGGCTATTTTTT", "ab1.ba2", "72", "72", "217", "288", "289",
                         "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0", "4081",
                         "4098", "5", "10", "", ""),
-                       ("", "", "ATCAGCCATGGCTATTTTTT", "ab2.ba1", "153", "164", "217", "260", "289",
+                       ("", "", "", "ATCAGCCATGGCTATTTTTT", "ab2.ba1", "153", "164", "217", "260", "289",
                         "1", "1", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "1", "1", "0", "0", "0", "0", "4081",
                         "4098", "5", "10", "", "")],
-                      [("chr5-11068-C-G", "2.5", "ATTGAAAGAATAACCCACAC", "ab1.ba2", "1", "100", "255", "276", "269",
+                      [("chr5-11068-C-G", "2.5", "alt", "ATTGAAAGAATAACCCACAC", "ab1.ba2", "1", "100", "255", "276", "269",
                         "5", "6", "0", "6", "0", "0", "5", "6", "0", "0", "0", "1", "0", "0", "0", "0", "5", "0", "1", "1", "5348", "5350", "", ""),
-                       ("", "", "AAAAAAAGAATAACCCACAC", "ab2.ba1", None, None, None, None,
+                       ("", "", "", "AAAAAAAGAATAACCCACAC", "ab2.ba1", None, None, None, None,
                         "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0",
                         "0", "0", "0", "0", "0", "1", "1", "5348", "5350", "", "")],
-                      [("chr5-10776-G-T", "3.1", "ATGCCTACCTCATTTGTCGT", "ab1.ba2", "46", "15", "287", "288", "290",
+                      [("chr5-10776-G-T", "3.1", "alt", "ATGCCTACCTCATTTGTCGT", "ab1.ba2", "46", "15", "287", "288", "290",
                         "3", "3", "3", "2", "3", "1", "0", "1", "1", "0.5", "0", "0.5", "0", "0", "0", "1",
                         "0", "0", "3", "3", "47170", "41149", "", ""),
-                       ("", "", "ATGCCTACCTCATTTGTCGT", "ab2.ba1", None, "274", None,
+                       ("", "", "", "ATGCCTACCTCATTTGTCGT", "ab2.ba1", None, "274", None,
                         "288", "290", "0", "3", "0", "2", "0", "1", "0", "1", None, "0.5", None, "0.5",
                         "0", "0", "0", "1", "0", "0", "3", "3", "47170", "41149", "", "")],
-                      [("chr5-11315-C-T", "3.2", "ACAACATCACGTATTCAGGT", "ab1.ba2", "197", "197", "240", "255", "271",
+                      [("chr5-11315-C-T", "3.2", "alt", "ACAACATCACGTATTCAGGT", "ab1.ba2", "197", "197", "240", "255", "271",
                         "2", "3", "2", "3", "0", "1", "2", "2", "0", "0.333333333333333", "1",
                         "0.666666666666667", "0", "0", "0", "0", "0", "0", "1", "1", "6584", "6482", "", ""),
-                       ("", "", "ACAACATCACGTATTCAGGT", "ab2.ba1", "35", "35", "240", "258", "271",
+                       ("", "", "", "ACAACATCACGTATTCAGGT", "ab2.ba1", "35", "35", "240", "258", "271",
                         "2", "3", "2", "3", "0", "1", "2", "2", "0", "0.333333333333333", "1",
                         "0.666666666666667", "0", "0", "0", "0", "0", "0", "1", "1", "6584", "6482", "", "")],
-                      [("chr5-13983-G-C", "4", "AAAAAAAGAATAACCCACAC", "ab1.ba2", "1", "100", "255", "276", "269",
+                      [("chr5-13983-G-C", "4", "alt", "AAAAAAAGAATAACCCACAC", "ab1.ba2", "1", "100", "255", "276", "269",
                         "5", "6", "0", "6", "0", "0", "5", "6", "0", "0", "0", "1", "0", "0", "0", "0", "5", "0", "1", "1", "5348", "5350", "", ""),
-                       ("", "", "AAAAAAAGAATAACCCACAC", "ab2.ba1", None, None, None, None,
+                       ("", "", "", "AAAAAAAGAATAACCCACAC", "ab2.ba1", None, None, None, None,
                         "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0",
                         "0", "0", "0", "0", "0", "1", "1", "5348", "5350", "", "")],
                       [("" * 34), ("" * 34)], [("" * 34), ("" * 34)], [("" * 34), ("" * 34)], [("" * 34), ("" * 34)], [("" * 34), ("" * 34)],
-                      [("chr5-13963-T-C", "6", "TTTTTAAGAATAACCCACAC", "ab1.ba2", "38", "38", "240", "283", "263",
+                      [("chr5-13963-T-C", "6", "alt", "TTTTTAAGAATAACCCACAC", "ab1.ba2", "38", "38", "240", "283", "263",
                         "110", "54", "110", "54", "0", "0", "110", "54", "0", "0", "1", "1", "0", "0", "0",
                         "0", "0", "0", "1", "1", "5348", "5350", "", ""),
-                       ("", "", "TTTTTAAGAATAACCCACAC", "ab2.ba1", "100", "112", "140", "145", "263",
+                       ("", "", "", "TTTTTAAGAATAACCCACAC", "ab2.ba1", "100", "112", "140", "145", "263",
                         "7", "12", "7", "12", "7", "12", "0", "0", "1", "1", "0",
                         "0", "0", "0", "0", "0", "0", "0", "1", "1", "5348", "5350", "", "")],
-                      [("chr5-13983-G-C", "7", "ATGTTGTGAATAACCCACAC", "ab1.ba2", None, "186", None, "276", "269",
+                      [("chr5-13983-G-C", "7", "alt", "ATGTTGTGAATAACCCACAC", "ab1.ba2", None, "186", None, "276", "269",
                         "0", "6", "0", "6", "0", "0", "0", "6", "0", "0", "0", "1", "0", "0", "0", "0", "0",
                         "0", "1", "1", "5348", "5350", "", ""),
-                       ("", "", "ATGTTGTGAATAACCCACAC", "ab2.ba1", None, None, None, None,
+                       ("", "", "", "ATGTTGTGAATAACCCACAC", "ab2.ba1", None, None, None, None,
                         "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0",
                         "0", "0", "0", "0", "0", "1", "1", "5348", "5350", "", "")]]
 
@@ -1612,16 +1612,19 @@
         ex = examples_tiers[i]
         for k in range(len(ex)):
             ws3.write_row(start_row + 2 + row + i + k + 2, 0, ex[k])
-        ws3.conditional_format('L{}:M{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3), {'type': 'formula', 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2), 'format': format13, 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
-        ws3.conditional_format('L{}:M{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),
+        ws3.conditional_format('M{}:N{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3), 
+                               {'type': 'formula', 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2), 
+                                'format': format13, 
+                                'multi_range': 'M{}:N{} U{}:V{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
+        ws3.conditional_format('M{}:N{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),
                                {'type': 'formula', 'criteria': '=OR($B${}="2.1",$B${}="2.2", $B${}="2.3", $B${}="2.4", $B${}="2.5")'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 2),
                                 'format': format33,
-                                'multi_range': 'L{}:M{} T{}:U{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
-        ws3.conditional_format('L{}:M{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),
+                                'multi_range': 'M{}:N{} U{}:V{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
+        ws3.conditional_format('M{}:N{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3),
                                {'type': 'formula',
                                 'criteria': '=$B${}>="3"'.format(start_row + 2 + row + i + k + 2),
                                 'format': format23,
-                                'multi_range': 'L{}:M{} T{}:U{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
+                                'multi_range': 'M{}:N{} U{}:V{} B{}'.format(start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3, start_row + 2 + row + i + k + 2, start_row + 2 + row + i + k + 3)})
         row += 3
     workbook.close()
     workbook2.close()
Binary file test-data/Variant_Analyzer_allele_frequencies_test.xlsx has changed
--- a/test-data/Variant_Analyzer_summary_test.csv	Wed Jul 27 08:59:00 2022 +0000
+++ b/test-data/Variant_Analyzer_summary_test.csv	Fri Aug 05 08:23:34 2022 +0000
@@ -1,10 +1,6 @@
 variant ID,tier,allele,tag,mate,read pos.ab,read pos.ba,read median length.ab,read median length.ba,DCS median length,FS.ab,FS.ba,FSqc.ab,FSqc.ba,ref.ab,ref.ba,alt.ab,alt.ba,rel. ref.ab,rel. ref.ba,rel. alt.ab,rel. alt.ba,na.ab,na.ba,lowq.ab,lowq.ba,trim.ab,trim.ba,SSCS alt.ab,SSCS alt.ba,SSCS ref.ab,SSCS ref.ba,in phase,chimeric tag
 ACH_TDII_5regions-505-C-A,2.1,alt,GATAACCTTGCTTCGTGATTAATC,ab1.ba2,132.0,131.0,264.0,263.0,173.0,1,3,1,3,0,0,1,3,0,0,1.0,1.0,0,0,0,0,0,0,2,1,1,1,,
 ,,,GATAACCTTGCTTCGTGATTAATC,ab2.ba1,,,,,173.0,0,0,0,0,0,0,0,0,,,,,0,0,0,0,0,0,2,1,1,1,,
-ACH_TDII_5regions-505-C-A,1.1,ref,GATTGGATAACGTTGTGGCAATTG,ab1.ba2,73.0,152.0,205.0,284.0,173.0,3,5,3,5,3,5,0,0,1.0,1.0,0,0,0,0,0,0,0,0,2,1,1,1,,
-,,,GATTGGATAACGTTGTGGCAATTG,ab2.ba1,198.0,198.0,263.5,283.0,173.0,4,3,4,3,4,3,0,0,1.0,1.0,0,0,0,0,0,0,0,0,2,1,1,1,,
-ACH_TDII_5regions-571-C-T,2.1,ref,GATAACCTTGCTTCGTGATTAATC,ab1.ba2,198.0,197.0,264.0,263.0,143.0,1,3,1,3,1,3,0,0,1.0,1.0,0,0,0,0,0,0,0,0,1,1,2,1,,
-,,,GATAACCTTGCTTCGTGATTAATC,ab2.ba1,,,,,143.0,0,0,0,0,0,0,0,0,,,,,0,0,0,0,0,0,1,1,2,1,,
 ACH_TDII_5regions-571-C-T,1.1,alt,GATTGGATAACGTTGTGGCAATTG,ab1.ba2,129.0,218.0,195.0,284.0,143.0,4,5,4,5,0,0,4,5,0,0,1.0,1.0,0,0,0,0,0,0,1,1,2,1,,
 ,,,GATTGGATAACGTTGTGGCAATTG,ab2.ba1,264.0,264.0,278.5,283.5,143.0,2,2,2,2,0,0,2,2,0,0,1.0,1.0,0,0,0,0,0,0,1,1,2,1,,
 ACH_TDII_5regions-958-T-C,2.4,alt,CCTCCCGGCAGTGCGAAAATGTCA,ab1.ba2,,,,,195.0,0,0,0,0,0,0,0,0,,,,,0,0,0,0,0,0,1,1,1,0,,
Binary file test-data/Variant_Analyzer_summary_test.xlsx has changed
Binary file test-data/Variant_Analyzer_tiers_test.xlsx has changed