Mercurial > repos > mheinzl > variant_analyzer2
changeset 4:386438cd4c3b draft
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 27 Oct 2020 12:39:21 +0000 |
| parents | 4fc62ab6e9e8 |
| children | d9cbf833624e |
| files | read2mut.py read2mut.xml |
| diffstat | 2 files changed, 14 insertions(+), 10 deletions(-) [+] |
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--- a/read2mut.py Sat Oct 17 09:11:53 2020 +0000 +++ b/read2mut.py Tue Oct 27 12:39:21 2020 +0000 @@ -231,7 +231,7 @@ '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', - 'other mut', 'chimeric tag') + 'in phase', 'chimeric tag') ws1.write_row(0, 0, header_line) counter_tier11 = 0 @@ -320,10 +320,11 @@ if add_mut1 > 1: for k, v in mut_read_dict[(key2[:-5] + '.ab.1')].items(): if k != key1: + new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] if len(add_mut14) == 0: - add_mut14 = str(k) + "_" + v + add_mut14 = new_mut else: - add_mut14 = add_mut14 + ", " + str(k) + "_" + v + add_mut14 = add_mut14 + ", " + new_mut else: k1 = [] else: @@ -362,10 +363,11 @@ if add_mut2 > 1: for k, v in mut_read_dict[(key2[:-5] + '.ab.2')].items(): if k != key1: + new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] if len(add_mut23) == 0: - add_mut23 = str(k) + "_" + v + add_mut23 = new_mut else: - add_mut23 = add_mut23 + ", " + str(k) + "_" + v + add_mut23 = add_mut23 + ", " + new_mut else: k2 = [] else: @@ -403,10 +405,11 @@ if add_mut3 > 1: for k, v in mut_read_dict[(key2[:-5] + '.ba.1')].items(): if k != key1 and k not in k2: + new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] if len(add_mut23) == 0: - add_mut23 = str(k) + "_" + v + add_mut23 = new_mut else: - add_mut23 = add_mut23 + ", " + str(k) + "_" + v + add_mut23 = add_mut23 + ", " + new_mut else: total3 = total3new = na3 = lowq3 = 0 ref3 = alt3 = ref3f = alt3f = 0 @@ -441,10 +444,11 @@ if add_mut4 > 1: for k, v in mut_read_dict[(key2[:-5] + '.ba.2')].items(): if k != key1 and k not in k1: + new_mut = str(k).split("#")[0] + "-" + str(int(str(k).split("#")[1]) + 1) + "-" + v[1] + "-" + v[0] if len(add_mut14) == 0: - add_mut14 = str(k) + "_" + v + add_mut14 = new_mut else: - add_mut14 = add_mut14 + ", " + str(k) + "_" + v + add_mut14 = add_mut14 + ", " + new_mut else: total4 = total4new = na4 = lowq4 = 0 ref4 = alt4 = ref4f = alt4f = 0
--- a/read2mut.xml Sat Oct 17 09:11:53 2020 +0000 +++ b/read2mut.xml Tue Oct 27 12:39:21 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.4" profile="19.01"> +<tool id="read2mut" name="Call specific mutations in reads:" version="1.0.5" profile="19.01"> <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description> <macros> <import>va_macros.xml</import>