Mercurial > repos > mheinzl > variant_analyzer2

changeset 67:60e813039aae draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Thu, 18 Mar 2021 10:42:19 +0000
parents d20be7e66378
children 4dfed0998184
files read2mut.py
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/read2mut.py	Thu Mar 18 10:35:14 2021 +0000
+++ b/read2mut.py	Thu Mar 18 10:42:19 2021 +0000
@@ -1195,7 +1195,7 @@
 	
     # sheet 2
     if chimera_correction:
-        header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)',
+        header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.5)', 'AC alt (tiers 1.1-2.5)', 'AF (tiers 1.1-2.5)', 'chimera-corrected cvrg (tiers 1.1-2.5)', 'chimeras in AC alt (tiers 1.1-2.5)', 'chimera-corrected AF (tiers 1.1-2.5)', 'AC alt (orginal DCS)', 'AF (original DCS)',
                     'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', 'tier 2.5',
                     'tier 3.1', 'tier 3.2', 'tier 4', 'tier 5.1', 'tier 5.2', 'tier 5.3', 'tier 5.4', 'tier 5.5', 'tier 6', 'tier 7', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2',
                     'AF 1.1-2.3', 'AF 1.1-2.4', 'AF 1.1-2.5', 'AF 1.1-3.1', 'AF 1.1-3.2', 'AF 1.1-4', 'AF 1.1-5.1', 'AF 1.1-5.2', 'AF 1.1-5.3', 'AF 1.1-5.4', 'AF 1.1-5.5', 'AF 1.1-6', 'AF 1.1-7')
@@ -1240,7 +1240,7 @@
                 if fraction_chimeras is None:
                     fraction_chimeras = 0.
                 new_cvrg = (cvrg - sum(used_tiers[-10:])) * (1. - fraction_chimeras)
-                lst.extend([chimeras_all, new_cvrg, safe_div(new_alt, new_cvrg)])
+                lst.extend([new_cvrg, chimeras_all, safe_div(new_alt, new_cvrg)])
             lst.extend([alt_count, safe_div(alt_count, cvrg)])
             lst.extend(used_tiers)
             lst.extend(cum_af)