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author | Pjotr Prins | 2021-01-02 14:54:34 +0000 |
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committer | Pjotr Prins | 2021-01-02 14:54:34 +0000 |
commit | 3bbe6652e4fca12c6782d005b079eab80893393c (patch) | |
tree | 9a667156c0f1c712c2f62c247f4504c8e0938e13 /workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py | |
parent | bb503e3835846d76f00359c71e7cd65f815f5a3e (diff) | |
download | bh20-seq-resource-3bbe6652e4fca12c6782d005b079eab80893393c.tar.gz bh20-seq-resource-3bbe6652e4fca12c6782d005b079eab80893393c.tar.lz bh20-seq-resource-3bbe6652e4fca12c6782d005b079eab80893393c.zip |
GenBank date parsing
Diffstat (limited to 'workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py')
-rwxr-xr-x | workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py | 10 |
1 files changed, 6 insertions, 4 deletions
diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py index c4e3eba..ebdf17e 100755 --- a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py +++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py @@ -40,6 +40,7 @@ for xmlfn in args.files: for gb in tree.findall('./GBSeq'): valid = None error = None + meta = {} id = gb.find("GBSeq_locus").text basename = dir+"/"+id print(f" parsing {id}") @@ -54,14 +55,15 @@ for xmlfn in args.files: f2.write(seq) # print(seq) except genbank.GBError as e: - print(f"OS error: {e}") + error = f"{e} for {id}" + print(error,file=sys.stderr) valid = False - error = str(e) state = {} - if not valid: - state['valid'] = False + state['valid'] = valid if error: state['error'] = error + if meta['warnings']: + state['warnings'] = meta['warnings'] states[id] = state print(states) |