diff options
Diffstat (limited to 'workflows/pull-data/genbank/ref.py')
| -rw-r--r-- | workflows/pull-data/genbank/ref.py | 35 |
1 files changed, 0 insertions, 35 deletions
diff --git a/workflows/pull-data/genbank/ref.py b/workflows/pull-data/genbank/ref.py index f803112..e998d37 100644 --- a/workflows/pull-data/genbank/ref.py +++ b/workflows/pull-data/genbank/ref.py @@ -1,40 +1,5 @@ # ---- BELOW IS JUST FOR REFERENCE ---- - -min_len_to_count = 15000 -num_seq_with_len_ge_X_bp = 0 - -missing_value_list = [] -not_created_accession_dict = {} -accession_with_errors_list = [] -if None: - - tree = ET.parse(path_metadata_xxx_xml) - GBSet = tree.getroot() - - for GBSeq in GBSet: - accession_version = GBSeq.find('GBSeq_accession-version').text - - try: - info = { - 'id': 'placeholder', - 'host': {}, - 'sample': {}, - 'virus': {}, - 'technology': {}, - 'submitter': {} - } - - sample['sample_id'] = accession_version - sample['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now - - # submitter info - GBSeq_references = GBSeq.find('GBSeq_references') - if GBSeq_references is not None: - author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')] - if len(author_list) > 0: - submitter['authors'] = author_list - GBReference = GBSeq_references.find('GBReference') if GBReference is not None: GBReference_journal = GBReference.find('GBReference_journal') |