genbank: split script

2 files changed, 166 insertions, 167 deletions

diff --git a/workflows/pull-data/genbank/genbank_pull.py b/workflows/pull-data/genbank/genbank_pull.py
new file mode 100755
index 0000000..07bb15d
--- /dev/null
+++ b/workflows/pull-data/genbank/genbank_pull.py
@@ -0,0 +1,166 @@
+#!/usr/bin/env python3
+#
+# - bulk download genbank data and matadata, preparing the FASTA and
+#   the YAML files
+#
+# See .guix-run python3 from_genbank_to_fasta_and_yaml.py
+
+import argparse
+parser = argparse.ArgumentParser()
+parser.add_argument('--ids-to-ignore', type=str, help='file with ids to ignore in all steps, 1 id per line', required=False)
+parser.add_argument('--ids-to-consider', type=str, help='file with ids to consider in all steps, 1 id per line', required=False)
+parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
+parser.add_argument('--only-missing-ids', action='store_true', help='download only missing ids not already downloaded', required=False)
+parser.add_argument('--dict-ontology', type=str, help='where is the ontology',
+                    default='../dict_ontology_standardization/', required=False)
+args = parser.parse_args()
+
+from Bio import Entrez
+Entrez.email = 'another_email@gmail.com'
+
+import xml.etree.ElementTree as ET
+import json
+import os
+import requests
+
+from datetime import date, datetime
+from dateutil.parser import parse
+
+import sys
+sys.path.append('../')
+from utils import is_integer, chunks, check_and_get_ontology_dictionaries
+
+
+num_ids_for_request = 100
+min_acceptable_collection_date = datetime(2019, 12, 1)
+
+dir_metadata = 'metadata_from_nuccore'
+dir_fasta_and_yaml = 'fasta_and_yaml'
+dir_dict_ontology_standardization = args.dict_ontology
+
+today_date = date.today().strftime("%Y.%m.%d")
+path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
+
+
+field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization)
+
+
+if os.path.exists(dir_metadata):
+    print("The directory '{}' already exists.".format(dir_metadata))
+
+    if not args.skip_request:
+        print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata))
+        sys.exit(-1)
+
+
+accession_to_ignore_set = set()
+
+if args.ids_to_ignore:
+    if not os.path.exists(args.ids_to_ignore):
+        print("\tThe '{}' file doesn't exist.".format(args.ids_to_ignore))
+        sys.exit(-1)
+
+    with open(args.ids_to_ignore) as f:
+        accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
+
+    print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set)))
+
+
+# ----------------------------------------------------------------------
+"""
+With --only-missing-ids only download accessions that we do not yet have!
+"""
+accession_already_downloaded_set = set()
+
+if os.path.exists(dir_fasta_and_yaml):
+    """
+    If the fasta_and_yaml directory exists and --only-missing-ids was set
+    we make a list of all downloaded accessions:
+    """
+    print("The directory '{}' already exists.".format(dir_fasta_and_yaml))
+    if not args.only_missing_ids:
+        print("To start the download, delete the directory '{}' or specify --only-missing-ids.".format(dir_fasta_and_yaml))
+        sys.exit(-1)
+
+    """
+    Fetch all YAML filenames and load `accession_already_downloaded_set`
+    """
+    accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')])
+    print('There are {} accessions already downloaded.'.format(len(accession_already_downloaded_set)))
+
+accession_to_ignore_set.update(accession_already_downloaded_set)
+
+# ----------------------------------------------------------------------
+"""
+Check for --ids-to-consider
+"""
+accession_to_consider_set = set()
+
+if args.ids_to_consider:
+    if not os.path.exists(args.ids_to_consider):
+        print("\tThe '{}' file doesn't exist.".format(args.ids_to_consider))
+        sys.exit(-1)
+
+    with open(args.ids_to_consider) as f:
+        accession_to_consider_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
+
+    if len(accession_to_consider_set) > 0:
+        print('There are {} accessions to consider.'.format(len(accession_to_consider_set)))
+
+# ----------------------------------------------------------------------
+"""
+Download section for genbank XML
+"""
+
+if not os.path.exists(dir_metadata):
+    # Take all the ids
+    id_set = set()
+
+    # Try to search several strings
+    term_list = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
+    for term in term_list:
+        tmp_list = Entrez.read(
+            Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
+        )['IdList']
+
+        # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
+        # Remove the version in the id
+        new_ids_set = set([x.split('.')[0] for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']])
+
+        if len(accession_to_consider_set) > 0:
+            new_ids_set = new_ids_set.intersection(accession_to_consider_set)
+
+        new_ids = len(new_ids_set.difference(id_set))
+        id_set.update(new_ids_set)
+
+        print('Term:', term, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
+
+    if not os.path.exists(path_ncbi_virus_accession):
+        r = requests.get('https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id')
+        with open(path_ncbi_virus_accession, 'w') as fw:
+            fw.write(r.text)
+
+    with open(path_ncbi_virus_accession) as f:
+        tmp_list = [line.strip('\n') for line in f]
+
+    new_ids_set = set(tmp_list)
+    if len(accession_to_consider_set) > 0:
+        new_ids_set = new_ids_set.intersection(accession_to_consider_set)
+
+    new_ids = len(new_ids_set.difference(id_set))
+    id_set.update(new_ids_set)
+
+    print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
+
+    id_set = id_set.difference(accession_to_ignore_set)
+    print('There are {} missing IDs to download.'.format(len(id_set)))
+
+    os.makedirs(dir_metadata)
+    for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
+        path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i))
+        print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
+
+        with open(path_metadata_xxx_xml, 'w') as fw:
+            fw.write(
+                Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
+            )
diff --git a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py b/workflows/pull-data/genbank/transform_genbank2yamlfa.py
index 9b2c9eb..025b4d9 100755..100644
--- a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py
+++ b/workflows/pull-data/genbank/transform_genbank2yamlfa.py
@@ -1,170 +1,3 @@
-#!/usr/bin/env python3
-#
-# - bulk download genbank data and matadata, preparing the FASTA and
-#   the YAML files
-#
-# See .guix-run python3 from_genbank_to_fasta_and_yaml.py
-
-import argparse
-parser = argparse.ArgumentParser()
-parser.add_argument('--ids-to-ignore', type=str, help='file with ids to ignore in all steps, 1 id per line', required=False)
-parser.add_argument('--ids-to-consider', type=str, help='file with ids to consider in all steps, 1 id per line', required=False)
-parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
-parser.add_argument('--only-missing-ids', action='store_true', help='download only missing ids not already downloaded', required=False)
-parser.add_argument('--dict-ontology', type=str, help='where is the ontology',
-                    default='../dict_ontology_standardization/', required=False)
-args = parser.parse_args()
-
-from Bio import Entrez
-Entrez.email = 'another_email@gmail.com'
-
-import xml.etree.ElementTree as ET
-import json
-import os
-import requests
-
-from datetime import date, datetime
-from dateutil.parser import parse
-
-import sys
-sys.path.append('../')
-from utils import is_integer, chunks, check_and_get_ontology_dictionaries
-
-
-num_ids_for_request = 100
-min_acceptable_collection_date = datetime(2019, 12, 1)
-
-dir_metadata = 'metadata_from_nuccore'
-dir_fasta_and_yaml = 'fasta_and_yaml'
-dir_dict_ontology_standardization = args.dict_ontology
-
-today_date = date.today().strftime("%Y.%m.%d")
-path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
-
-
-field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization)
-
-
-if os.path.exists(dir_metadata):
-    print("The directory '{}' already exists.".format(dir_metadata))
-
-    if not args.skip_request:
-        print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata))
-        sys.exit(-1)
-
-
-accession_to_ignore_set = set()
-
-if args.ids_to_ignore:
-    if not os.path.exists(args.ids_to_ignore):
-        print("\tThe '{}' file doesn't exist.".format(args.ids_to_ignore))
-        sys.exit(-1)
-
-    with open(args.ids_to_ignore) as f:
-        accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
-
-    print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set)))
-
-
-# ----------------------------------------------------------------------
-"""
-With --only-missing-ids only download accessions that we do not yet have!
-"""
-accession_already_downloaded_set = set()
-
-if os.path.exists(dir_fasta_and_yaml):
-    """
-    If the fasta_and_yaml directory exists and --only-missing-ids was set
-    we make a list of all downloaded accessions:
-    """
-    print("The directory '{}' already exists.".format(dir_fasta_and_yaml))
-    if not args.only_missing_ids:
-        print("To start the download, delete the directory '{}' or specify --only-missing-ids.".format(dir_fasta_and_yaml))
-        sys.exit(-1)
-
-    """
-    Fetch all YAML filenames and load `accession_already_downloaded_set`
-    """
-    accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')])
-    print('There are {} accessions already downloaded.'.format(len(accession_already_downloaded_set)))
-
-accession_to_ignore_set.update(accession_already_downloaded_set)
-
-# ----------------------------------------------------------------------
-"""
-Check for --ids-to-consider
-"""
-accession_to_consider_set = set()
-
-if args.ids_to_consider:
-    if not os.path.exists(args.ids_to_consider):
-        print("\tThe '{}' file doesn't exist.".format(args.ids_to_consider))
-        sys.exit(-1)
-
-    with open(args.ids_to_consider) as f:
-        accession_to_consider_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
-
-    if len(accession_to_consider_set) > 0:
-        print('There are {} accessions to consider.'.format(len(accession_to_consider_set)))
-
-# ----------------------------------------------------------------------
-"""
-Download section for genbank XML
-"""
-
-if not os.path.exists(dir_metadata):
-    # Take all the ids
-    id_set = set()
-
-    # Try to search several strings
-    term_list = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
-    for term in term_list:
-        tmp_list = Entrez.read(
-            Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
-        )['IdList']
-
-        # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
-        # Remove the version in the id
-        new_ids_set = set([x.split('.')[0] for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']])
-
-        if len(accession_to_consider_set) > 0:
-            new_ids_set = new_ids_set.intersection(accession_to_consider_set)
-
-        new_ids = len(new_ids_set.difference(id_set))
-        id_set.update(new_ids_set)
-
-        print('Term:', term, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
-
-    if not os.path.exists(path_ncbi_virus_accession):
-        r = requests.get('https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id')
-        with open(path_ncbi_virus_accession, 'w') as fw:
-            fw.write(r.text)
-
-    with open(path_ncbi_virus_accession) as f:
-        tmp_list = [line.strip('\n') for line in f]
-
-    new_ids_set = set(tmp_list)
-    if len(accession_to_consider_set) > 0:
-        new_ids_set = new_ids_set.intersection(accession_to_consider_set)
-
-    new_ids = len(new_ids_set.difference(id_set))
-    id_set.update(new_ids_set)
-
-    print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
-
-    id_set = id_set.difference(accession_to_ignore_set)
-    print('There are {} missing IDs to download.'.format(len(id_set)))
-
-    os.makedirs(dir_metadata)
-    for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
-        path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i))
-        print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
-
-        with open(path_metadata_xxx_xml, 'w') as fw:
-            fw.write(
-                Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
-            )
-
 # ----------------------------------------------------------------------
 """
 Generate metadata (YAML) and FASTA files for each accession