From 8cb542fdf60273aec7ec107f8bc4896375381263 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Fri, 10 Jul 2020 13:55:49 +0200 Subject: an output file is created with the accessions for which no YAML file is created --- .../download_genbank_data/from_genbank_to_fasta_and_yaml.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'scripts/download_genbank_data') diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 39e401a..d5b0ffd 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -138,6 +138,7 @@ min_len_to_count = 27500 num_seq_with_len_ge_X_bp = 0 missing_value_list = [] +not_created_accession_list = [] accession_with_errors_list = [] for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]: @@ -371,7 +372,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: - print(accession_version, ' - technology not found') + #print(accession_version, ' - technology not found') + not_created_accession_list.append([accession_version, 'technology not found']) continue with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw: @@ -400,4 +402,10 @@ if len(accession_with_errors_list) > 0: with open(path_accession_with_errors_tsv, 'w') as fw: fw.write('\n'.join(accession_with_errors_list)) +if len(not_created_accession_list) > 0: + path_not_created_accession_tsv = 'not_created_accession.tsv' + print('Written not created accession in {}'.format(path_not_created_accession_tsv)) + with open(path_not_created_accession_tsv, 'w') as fw: + fw.write('\n'.join(['\t'.join(x) for x in not_created_accession_list])) + print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp)) -- cgit v1.2.3