Mercurial > repos > mheinzl > variant_analyzer2
changeset 77:1797e461d674 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Mon, 29 Mar 2021 09:22:57 +0000 |
| parents | 56f271641828 |
| children | fdfe9a919ff7 |
| files | read2mut.py |
| diffstat | 1 files changed, 21 insertions(+), 5 deletions(-) [+] |
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--- a/read2mut.py Fri Mar 26 07:49:15 2021 +0000 +++ b/read2mut.py Mon Mar 29 09:22:57 2021 +0000 @@ -320,7 +320,7 @@ ref = mut_array[i, 2] alt = mut_array[i, 3] dcs_median = cvrg_dict[key1][2] - whole_array = pure_tags_dict_short[key1].keys() + whole_array = list(pure_tags_dict_short[key1].keys()) tier_dict[key1] = {} values_tier_dict = [("tier 1.1", 0), ("tier 1.2", 0), ("tier 2.1", 0), ("tier 2.2", 0), ("tier 2.3", 0), ("tier 2.4", 0), ("tier 2.5", 0), @@ -604,7 +604,11 @@ # mate 1 - SSCS ab softclipped_idx1 = [True if re.search(r"^[0-9]+S", string) or re.search(r"S$", string) else False for string in cigars_dcs1] - ratio1 = safe_div(sum(softclipped_idx1), float(len(softclipped_idx1))) >= threshold_reads + safe_div_result = safe_div(sum(softclipped_idx1), float(len(softclipped_idx1))) + if (safe_div_result == None): + ratio1 = False + else: + ratio1 = safe_div_result >= threshold_reads if any(ij is True for ij in softclipped_idx1): softclipped_both_ends_idx1 = [True if (re.search(r"^[0-9]+S", string) and re.search(r"S$", string)) else False for string in cigars_dcs1] softclipped_start1 = [int(string.split("S")[0]) if re.search(r"^[0-9]+S", string) else -1 for string in cigars_dcs1] @@ -624,7 +628,11 @@ # mate 1 - SSCS ba softclipped_idx4 = [True if re.search(r"^[0-9]+S", string) or re.search(r"S$", string) else False for string in cigars_dcs4] - ratio4 = safe_div(sum(softclipped_idx4), float(len(softclipped_idx4))) >= threshold_reads + safe_div_result = safe_div(sum(softclipped_idx4), float(len(softclipped_idx4))) + if (safe_div_result == None): + ratio4 = False + else: + ratio4 = safe_div_result >= threshold_reads if any(ij is True for ij in softclipped_idx4): softclipped_both_ends_idx4 = [True if (re.search(r"^[0-9]+S", string) and re.search(r"S$", string)) else False for string in cigars_dcs4] softclipped_start4 = [int(string.split("S")[0]) if re.search(r"^[0-9]+S", string) else -1 for string in cigars_dcs4] @@ -644,7 +652,11 @@ # mate 2 - SSCS ab softclipped_idx2 = [True if re.search(r"^[0-9]+S", string) or re.search(r"S$", string) else False for string in cigars_dcs2] - ratio2 = safe_div(sum(softclipped_idx2), float(len(softclipped_idx2))) >= threshold_reads + safe_div_result = safe_div(sum(softclipped_idx2), float(len(softclipped_idx2))) + if (safe_div_result == None): + ratio2 = False + else: + ratio2 = safe_div_result >= threshold_reads if any(ij is True for ij in softclipped_idx2): softclipped_both_ends_idx2 = [True if (re.search(r"^[0-9]+S", string) and re.search(r"S$", string)) else False for string in cigars_dcs2] softclipped_start2 = [int(string.split("S")[0]) if re.search(r"^[0-9]+S", string) else -1 for string in cigars_dcs2] @@ -664,7 +676,11 @@ # mate 2 - SSCS ba softclipped_idx3 = [True if re.search(r"^[0-9]+S", string) or re.search(r"S$", string) else False for string in cigars_dcs3] - ratio3 = safe_div(sum(softclipped_idx3), float(len(softclipped_idx3))) >= threshold_reads + safe_div_result = safe_div(sum(softclipped_idx3), float(len(softclipped_idx3))) + if (safe_div_result == None): + ratio3 = False + else: + ratio3 = safe_div_result >= threshold_reads if any(ij is True for ij in softclipped_idx3): softclipped_both_ends_idx3 = [True if (re.search(r"^[0-9]+S", string) and re.search(r"S$", string)) else False for string in cigars_dcs3] softclipped_start3 = [int(string.split("S")[0]) if re.search(r"^[0-9]+S", string) else -1 for string in cigars_dcs3]