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| author | AndreaGuarracino | 2020-09-04 12:34:54 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-09-04 12:34:54 +0200 |
| commit | c754aab95f47317228a07ccbe3818780aa22a52a (patch) | |
| tree | c6c067f20d41eb8259e04c8709569d05f7ff6f5b | |
| parent | 8417375cd86c6ba2f29511964544a267ed883ccd (diff) | |
| download | bh20-seq-resource-c754aab95f47317228a07ccbe3818780aa22a52a.tar.gz bh20-seq-resource-c754aab95f47317228a07ccbe3818780aa22a52a.tar.lz bh20-seq-resource-c754aab95f47317228a07ccbe3818780aa22a52a.zip | |
fixed bugs in in index management and type conversion
| -rw-r--r-- | bh20sequploader/main.py | 4 | ||||
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 2 |
2 files changed, 3 insertions, 3 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 314a2ea..f8127af 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -47,8 +47,8 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): raise ValueError("It is possible to upload just one FASTA file at a time") target.append(qc_fasta(sequence_p2)) - target[0] = ("reads_1."+target[0][0][6:], target[0][1]) - target[1] = ("reads_2."+target[1][0][6:], target[0][1]) + target[0] = ("reads_1."+target[0][0][6:], target[0][1], target[0][2]) + target[1] = ("reads_2."+target[1][0][6:], target[1][1], target[1][2]) if do_qc and target[0][2] == 'text/fasta' and sample_id != target[0][1]: raise ValueError("The sample_id field in the metadata must be the same as the FASTA header") diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index 8866d01..b872896 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -198,7 +198,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): missing_value_list.append('\t'.join([accession, 'host_sex', VALUE_text])) elif TAG_text in ['host_age', 'host age']: if is_integer(VALUE_text): - info_for_yaml_dict['host']['host_age'] = VALUE_text + info_for_yaml_dict['host']['host_age'] = int(VALUE_text) info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036' elif TAG_text == 'collected_by': if VALUE_text.lower() not in ['not available', 'missing']: |