diff options
Diffstat (limited to 'workflows/pull-data/genbank')
| -rw-r--r-- | workflows/pull-data/genbank/.guix-run | 2 | ||||
| -rw-r--r-- | workflows/pull-data/genbank/genbank.py | 17 |
2 files changed, 7 insertions, 12 deletions
diff --git a/workflows/pull-data/genbank/.guix-run b/workflows/pull-data/genbank/.guix-run index 6db7871..f6b1a0c 100644 --- a/workflows/pull-data/genbank/.guix-run +++ b/workflows/pull-data/genbank/.guix-run @@ -4,5 +4,5 @@ echo # next run: echo 'export PATH=$GUIX_ENVIRONMENT/bin:$PATH' -~/.config/guix/current/bin/guix environment guix --ad-hoc python python-biopython python-requests python-dateutil ruby +~/.config/guix/current/bin/guix environment guix --ad-hoc python python-biopython python-requests python-dateutil ruby jq diff --git a/workflows/pull-data/genbank/genbank.py b/workflows/pull-data/genbank/genbank.py index 026c03f..a994055 100644 --- a/workflows/pull-data/genbank/genbank.py +++ b/workflows/pull-data/genbank/genbank.py @@ -90,10 +90,9 @@ def get_metadata(id, gbseq): except AttributeError: warn("Missing "+msg) - host.host_species = "http://purl.obolibrary.org/obo/NCBITaxon_9606" sample.sample_id = id sample.database = "https://www.ncbi.nlm.nih.gov/genbank/" - sample.source_database_accession = f"http://identifiers.org/insdc/{id}#sequence" + sample.source_database_accession = [ f"http://identifiers.org/insdc/{id}#sequence" ] # <GBQualifier_value>USA: Cruise_Ship_1, California</GBQualifier_value> n = fetch("host_species", ".//GBQualifier/GBQualifier_name/[.='country']/../GBQualifier_value") if n: sample.collection_location = n @@ -112,7 +111,7 @@ def get_metadata(id, gbseq): if n != 'Unpublished': institute,address = n.split(',',1) if ")" in institute: - submitter.submitter_name = institute.split(')')[1] + submitter.submitter_name = [institute.split(')')[1].strip()] submitter.submitter_address = address.strip() except AttributeError: pass @@ -129,13 +128,13 @@ def get_metadata(id, gbseq): # technology.assembly_method = 'http://purl.obolibrary.org/obo/GENEPIO_0001628' p = re.compile(r'.*Assembly Method :: ([^;]+).*') m = p.match(n) - if m: technology.alignment_protocol = m.group(1) + if m: technology.alignment_protocol = m.group(1).strip() p = re.compile(r'.*Coverage :: ([^;]+).*') m = p.match(n) if m: technology.sequencing_coverage = m.group(1) p = re.compile(r'.*Sequencing Technology :: ([^;]+).*') m = p.match(n) - if m: technology.sample_sequencing_technology = m.group(1).strip() + if m: technology.sample_sequencing_technology = [m.group(1).strip()] else: warn("Missing sample_sequencing_technology") # --- Dates @@ -167,10 +166,7 @@ def get_metadata(id, gbseq): n = fetch("host_species", ".//GBQualifier/GBQualifier_name/[.='host']/../GBQualifier_value") if n: list = n.split('; ') - species = list[0] - host.host_species = species - if species != "Homo sapiens": - warn(f"Species not understood: {species}") + host.host_species = list[0] if len(list)>1: sex = list[1] if 'male' in sex or 'gender: M' in sex: host.host_sex = 'male' @@ -183,13 +179,12 @@ def get_metadata(id, gbseq): if m: host.host_age = int(m.group(1)) host.host_age_unit = 'http://purl.obolibrary.org/obo/UO_0000036' - # sys.exit(1) n = fetch("virus_strain", ".//GBQualifier/GBQualifier_name/[.='isolate']/../GBQualifier_value") if n: virus.virus_strain = n n = fetch("virus_species", ".//GBQualifier/GBQualifier_name/[.='db_xref']/../GBQualifier_value") if n: virus.virus_species = "http://purl.obolibrary.org/obo/NCBITaxon_"+n.split('taxon:')[1] n = fetch("specimen_source", ".//GBQualifier/GBQualifier_name/[.='isolation_source']/../GBQualifier_value") - if n: sample.specimen_source = n + if n: sample.specimen_source = [n] info = { 'id': 'placeholder', |