Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 20:ac07ff15dcfd draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Mon, 22 Feb 2021 15:05:26 +0000 |
| parents | 858ca8b7ad43 |
| children | b67d4c7da780 |
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| 19:858ca8b7ad43 | 20:ac07ff15dcfd |
|---|---|
| 99 sys.exit("Error: Could not find '{}'".format(json_file)) | 99 sys.exit("Error: Could not find '{}'".format(json_file)) |
| 100 if thresh < 0: | 100 if thresh < 0: |
| 101 sys.exit("Error: thresh is '{}', but only non-negative integers allowed".format(thresh)) | 101 sys.exit("Error: thresh is '{}', but only non-negative integers allowed".format(thresh)) |
| 102 if phred_score < 0: | 102 if phred_score < 0: |
| 103 sys.exit("Error: phred is '{}', but only non-negative integers allowed".format(phred_score)) | 103 sys.exit("Error: phred is '{}', but only non-negative integers allowed".format(phred_score)) |
| 104 if trim < 0: | 104 if trim5 < 0: |
| 105 sys.exit("Error: trim is '{}', but only non-negative integers allowed".format(thresh)) | 105 sys.exit("Error: trim5 is '{}', but only non-negative integers allowed".format(trim5)) |
| 106 if trim3 < 0: | |
| 107 sys.exit("Error: trim3 is '{}', but only non-negative integers allowed".format(trim3)) | |
| 106 | 108 |
| 107 # load dicts | 109 # load dicts |
| 108 with open(json_file, "r") as f: | 110 with open(json_file, "r") as f: |
| 109 (tag_dict, cvrg_dict) = json.load(f) | 111 (tag_dict, cvrg_dict) = json.load(f) |
| 110 | 112 |