transform-genbank-xml2yamlfa.py rewrite

1 files changed, 62 insertions, 321 deletions

diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
index 8b970b6..c4e3eba 100755
--- a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
+++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
@@ -1,326 +1,67 @@
 #!/usr/bin/env python3
 #
 # Create a single YAML/FASTA from genbank XML
-
+#
+#   transform-genbank-xml2yamlfa --out ~/tmp/pubseq file(s)
+#
+# Also writes a validation file in the outdir named state.json
+#
+# Where --in can be a file or a directory
 # ----------------------------------------------------------------------
-"""
-Generate metadata (YAML) and FASTA files for each accession
-"""
-
-if not os.path.exists(dir_fasta_and_yaml):
-    os.makedirs(dir_fasta_and_yaml)
-
-min_len_to_count = 15000
-num_seq_with_len_ge_X_bp = 0
-
-missing_value_list = []
-not_created_accession_dict = {}
-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')]:
-    tree = ET.parse(path_metadata_xxx_xml)
-    GBSet = tree.getroot()
-
-    for GBSeq in GBSet:
-        accession_version = GBSeq.find('GBSeq_accession-version').text
-
-        GBSeq_sequence = GBSeq.find('GBSeq_sequence')
-        if GBSeq_sequence is None:
-            print(accession_version, ' - sequence not found')
-            continue
-
-        try:
-            # print(path_metadata_xxx_xml, accession_version)
-
-            # A general default-empty yaml could be read from the definitive one
-            info_for_yaml_dict = {
-                'id': 'placeholder',
-                'host': {},
-                'sample': {},
-                'virus': {},
-                'technology': {},
-                'submitter': {}
-            }
-
-
-            info_for_yaml_dict['sample']['sample_id'] = accession_version
-            info_for_yaml_dict['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:
-                    info_for_yaml_dict['submitter']['authors'] = author_list
-
-                GBReference = GBSeq_references.find('GBReference')
-                if GBReference is not None:
-                    GBReference_journal = GBReference.find('GBReference_journal')
-
-                    if GBReference_journal is not None and GBReference_journal.text != 'Unpublished':
-                        if 'Submitted' in GBReference_journal.text:
-                            info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(') ')[1].split(',')[0].strip())]
-                            info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip()
-                        else:
-                            info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text
-
-            # This script download and prepare data and metadata for assemblies samples
-            info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628'
-
-            GBSeq_comment = GBSeq.find('GBSeq_comment')
-            if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
-                prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly'
-
-                GBSeq_comment_text = GBSeq_comment.text.split(
-                    '{}-Data-START## ; '.format(prefix_split_string)
-                )[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0]
-
-                for info_to_check, field_in_yaml in zip(
-                    ['Assembly Method', 'Coverage', 'Sequencing Technology'],
-                    ['alignment_protocol', 'sequencing_coverage', 'sample_sequencing_technology']
-                ):
-                    if info_to_check in GBSeq_comment_text:
-                        tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
-                        if field_in_yaml == 'sequencing_coverage':
-                            # A regular expression would be better!
-                            try:
-                                info_for_yaml_dict['technology'][field_in_yaml] = [
-                                    float(tech_info_to_parse.replace('(average)', '').replace("reads/nt", '').
-                                          replace('(average for 6 sequences)', '').replace(',', '.').strip(' xX>'))
-                                ]
-                            except ValueError:
-                                print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
-                                pass
-                        elif field_in_yaml == 'sample_sequencing_technology':
-                            new_seq_tec_list = []
-                            for seq_tec in tech_info_to_parse.split(';'):
-                                seq_tec = seq_tec.strip()
-                                if seq_tec in field_to_term_to_uri_dict['ncbi_sequencing_technology']:
-                                    seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec]
-                                    new_seq_tec_list.append(seq_tec)
-                                else:
-                                    missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
-
-                            if len(new_seq_tec_list) > 0:
-                                info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list]
-                        else:
-                            info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
-
-
-            for GBFeature in GBSeq.iter('GBFeature'):
-                if GBFeature.find('GBFeature_key').text != 'source':
-                    continue
-
-                for GBQualifier in GBFeature.iter('GBQualifier'):
-                    GBQualifier_value = GBQualifier.find('GBQualifier_value')
-                    if GBQualifier_value is None:
-                        continue
-                    GBQualifier_value_text = GBQualifier_value.text
-
-                    GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
-
-                    if GBQualifier_name_text == 'host':
-                        GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female
-                        if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']:
-                            # Cases like 'Felis catus; Domestic Shorthair'
-                            info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text]
-                        else:
-                            GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
-
-                            if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']:
-                                info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text_list[0]]
-                            elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version):
-                                # Information checked manually from NCBI Virus
-                                info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species']['Canis lupus familiaris']
-                            else:
-                                missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]]))
-
-                            # Possible cases:
-                            # - Homo sapiens                        --> ['Homo sapiens']
-                            # - Homo sapiens; female                --> ['Homo sapiens', 'female']
-                            # - Homo sapiens; female 63             --> ['Homo sapiens', 'female 63']
-                            # - Homo sapiens; female; age 40        --> ['Homo sapiens', 'female', 'age 40']
-                            # - Homo sapiens; gender: F; age: 61    --> ['Homo sapiens', 'gender: F', 'age: 61']
-                            # - Homo sapiens; gender: M; age: 68    --> ['Homo sapiens', 'gender: M', 'age: 68']
-                            # - Homo sapiens; hospitalized patient  --> ['Homo sapiens', 'hospitalized patient']
-                            # - Homo sapiens; male                  --> ['Homo sapiens', 'male']
-                            # - Homo sapiens; male; 63              --> ['Homo sapiens', 'male', '63']
-                            # - Homo sapiens; male; age 29          --> ['Homo sapiens', 'male', 'age 29']
-                            # - Homo sapiens; symptomatic           --> ['Homo sapiens', 'symptomatic']
-                            if len(GBQualifier_value_text_list) > 1:
-                                host_sex = ''
-                                if 'female' in GBQualifier_value_text_list[1]:
-                                    host_sex = 'female'
-                                elif 'male' in GBQualifier_value_text_list[1]:
-                                    host_sex = 'male'
-                                elif 'gender' in GBQualifier_value_text_list[1]:
-                                    host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip()
-                                    if host_sex_one_lecter in ['F', 'M']:
-                                        host_sex = 'female' if host_sex_one_lecter == 'F' else 'male'
-
-                                if host_sex in ['male', 'female']:
-                                    info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
-                                elif GBQualifier_value_text_list[1] in field_to_term_to_uri_dict['ncbi_host_health_status']:
-                                    info_for_yaml_dict['host']['host_health_status'] = field_to_term_to_uri_dict['ncbi_host_health_status'][GBQualifier_value_text_list[1]]
-                                else:
-                                    missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]]))
-
-                                # Host age
-                                host_age = -1
-                                if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]):
-                                    host_age = int(GBQualifier_value_text_list[1].split(' ')[-1])
-                                elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]):
-                                    host_age = int(GBQualifier_value_text_list[2].split(' ')[-1])
-
-                                if host_age >= 0 and host_age < 110:
-                                    info_for_yaml_dict['host']['host_age'] = host_age
-                                    info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
-                                elif len(GBQualifier_value_text_list) > 2:
-                                    missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]]))
-                    elif GBQualifier_name_text == 'collected_by':
-                        if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
-                            info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
-                        else:
-                            info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
-                    elif GBQualifier_name_text == 'isolation_source':
-                        if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']:
-                            GBQualifier_value_text = GBQualifier_value_text.upper()  # For example, in case of 'usa: wa'
-
-                        # Little cleaning
-                        GBQualifier_value_text = GBQualifier_value_text.strip("/'")
-
-                        if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']:
-                            info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]]
-                        else:
-                            if GBQualifier_value_text.lower() in ['np/op', 'np-op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
-                            elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
-                            elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
-                            elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']]
-                            elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']]
-                            else:
-                                missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text]))
-                    elif GBQualifier_name_text == 'collection_date':
-                        # TO_DO: which format we will use?
-                        date_to_write = GBQualifier_value_text
-
-                        if len(GBQualifier_value_text.split('-')) == 1:
-                            if int(GBQualifier_value_text) < 2020:
-                                date_to_write = "{}-12-15".format(GBQualifier_value_text)
-                            else:
-                                date_to_write = "{}-01-15".format(GBQualifier_value_text)
-
-                            if 'additional_collection_information' in info_for_yaml_dict['sample']:
-                                info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
-                            else:
-                                info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
-                        elif len(GBQualifier_value_text.split('-')) == 2:
-                            date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m') + '-15'
-
-                            if 'additional_collection_information' in info_for_yaml_dict['sample']:
-                                info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
-                            else:
-                                info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text)
-                        elif len(GBQualifier_value_text.split('-')) == 3:
-                            GBQualifier_value_text_list = GBQualifier_value_text.split('-')
-
-                            if GBQualifier_value_text_list[1].isalpha():
-                                date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
-
-                        info_for_yaml_dict['sample']['collection_date'] = date_to_write
-                    elif GBQualifier_name_text in ['lat_lon', 'country']:
-                        if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text:
-                            GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':')
-
-                        if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_countries']:
-                            info_for_yaml_dict['sample']['collection_location'] = field_to_term_to_uri_dict['ncbi_countries'][GBQualifier_value_text]
-                        else:
-                            missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text]))
-                    elif GBQualifier_name_text == 'note':
-                        if 'additional_collection_information' in info_for_yaml_dict['sample']:
-                            info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text
-                        else:
-                            info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
-                    elif GBQualifier_name_text == 'isolate':
-                        info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
-                    elif GBQualifier_name_text == 'db_xref':
-                        info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
-
-            # Check if mandatory fields are missing
-            if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
-                # print(accession_version, ' - technology not found')
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('sample_sequencing_technology not found')
-
-            if 'collection_location' not in info_for_yaml_dict['sample']:
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('collection_location not found')
-
-            if 'collection_date' not in info_for_yaml_dict['sample']:
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('collection_date not found')
-            else:
-                year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')]
-
-                collection_date_in_yaml = datetime(year, month, day)
-                if collection_date_in_yaml < min_acceptable_collection_date:
-                    if accession_version not in not_created_accession_dict:
-                        not_created_accession_dict[accession_version] = []
-                    not_created_accession_dict[accession_version].append('collection_date too early')
-
-            if 'authors' not in info_for_yaml_dict['submitter']:
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('authors not found')
-
-            if 'host_species' not in info_for_yaml_dict['host']:
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('host_species not found')
-
-            if len(GBSeq_sequence.text) < min_len_to_count:
-                if accession_version not in not_created_accession_dict:
-                    not_created_accession_dict[accession_version] = []
-                not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count))
-
-            if accession_version not in not_created_accession_dict:
-                num_seq_with_len_ge_X_bp += 1
-
-                with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw:
-                    fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
-
-                with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw:
-                    json.dump(info_for_yaml_dict, fw, indent=2)
-        except:
-            print("Unexpected error for the ID {}: {}".format(accession_version, sys.exc_info()[0]))
-            accession_with_errors_list.append(accession_version)
-            continue
-
-if len(missing_value_list) > 0:
-    path_missing_terms_tsv = 'missing_terms.genbank.tsv'
-    print('Written missing terms in {}'.format(path_missing_terms_tsv))
-    with open(path_missing_terms_tsv, 'w') as fw:
-        fw.write('\n'.join(missing_value_list))
-
-if len(accession_with_errors_list) > 0:
-    path_accession_with_errors_tsv = 'accession_with_errors.genbank.tsv'
-    print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv))
-    with open(path_accession_with_errors_tsv, 'w') as fw:
-        fw.write('\n'.join(accession_with_errors_list))
-
-if len(not_created_accession_dict) > 0:
-    path_not_created_accession_tsv = 'not_created_accession.genbank.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([accession_version, ','.join(missing_info_list)]) for accession_version, missing_info_list in not_created_accession_dict.items()]))
 
-print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
+# See also directory .guix-run and README.md
+
+import argparse
+import gzip
+import os
+import sys
+import types
+import xml.etree.ElementTree as ET
+from utils import chunks
+import genbank
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--out', type=str, help='Directory to write to',
+required=True)
+parser.add_argument('files', nargs='+', help='file(s)')
+args = parser.parse_args()
+
+dir = args.out
+if not os.path.exists(dir):
+    raise Exception(f"Directory {dir} does not exist")
+
+states = {}
+
+for xmlfn in args.files:
+    print(f"--- Reading {xmlfn}")
+    with gzip.open(xmlfn, 'r') as f:
+        xml = f.read().decode()
+        tree = ET.fromstring(xml)
+        for gb in tree.findall('./GBSeq'):
+            valid = None
+            error = None
+            id = gb.find("GBSeq_locus").text
+            basename = dir+"/"+id
+            print(f"    parsing {id}")
+            try:
+                valid,meta = genbank.get_metadata(id,gb)
+                if valid:
+                    fa = basename+".fa"
+                    seq = genbank.get_sequence(id,gb)
+                    print(f"    writing {fa}")
+                    with open(fa,"w") as f2:
+                        f2.write(f"> {id}\n")
+                        f2.write(seq)
+                    # print(seq)
+            except genbank.GBError as e:
+                print(f"OS error: {e}")
+                valid = False
+                error = str(e)
+            state = {}
+            if not valid:
+                state['valid'] = False
+            if error:
+                state['error'] = error
+            states[id] = state
+
+print(states)