From 4cf8612774c3f5fd8e6e9eef88246d7338d50a79 Mon Sep 17 00:00:00 2001 From: kistlerk Date: Tue, 24 Mar 2020 13:40:29 -0700 Subject: [PATCH] fauna upload and download scripts for seasonal corona viruses --- builds/SEASONAL_CORONA.md | 16 + package-lock.json | 184 +- package.json | 6 +- source-data/seasonal_corona_date_fix.tsv | 3535 +++++++++++++++++ source-data/seasonal_corona_location_fix.tsv | 2 + .../seasonal_corona_strain_name_fix.tsv | 1 + vdb/seasonal_corona_download.py | 21 + vdb/seasonal_corona_upload.py | 139 + 8 files changed, 3809 insertions(+), 95 deletions(-) create mode 100644 builds/SEASONAL_CORONA.md create mode 100644 source-data/seasonal_corona_date_fix.tsv create mode 100644 source-data/seasonal_corona_location_fix.tsv create mode 100644 source-data/seasonal_corona_strain_name_fix.tsv create mode 100644 vdb/seasonal_corona_download.py create mode 100644 vdb/seasonal_corona_upload.py diff --git a/builds/SEASONAL_CORONA.md b/builds/SEASONAL_CORONA.md new file mode 100644 index 0000000..2335e51 --- /dev/null +++ b/builds/SEASONAL_CORONA.md @@ -0,0 +1,16 @@ +## Download data from Vipr + +* [Vipr search URL](https://www.viprbrc.org/brc/vipr_genome_search.spg?method=ModifySearch&selectionContext=1584731753653) +* This is search fields of `genome[data to return] AND human[host] under Coronaviridae` +* Select all results. Download as `Genome FASTA` and select `Custom Format`, then add all possible FASTA fields in the order: `genbank_accession|strain_name|segment|date|host|country|subtype|virus_species` +* Download the file as `human_cov_genome.fasta` and save it in the fauna/data/ directory +* By default, `seasonal_corona_upload.py` will try to upload full length sequencing data (the `human_cov_genome.fasta` file downloaded from Vipr) AND gene-only sequences for Spike and HE (obtained through alignment of full-length sequences). Download these files from the [seasonal-corona repo](https://www.github.com/nextstrain/seasonal-corona/starter_data) and save them in the fauna/data/ directory +* If you DO NOT wish to upload gene-only sequences, add `--vipr_upload` to the command below. If you wish to ONLY upload gene sequences (not full length) add `--gene_upload` to the command below + +## Upload to fauna + +`python2 vdb/seasonal_corona_upload.py -db vdb -v seasonal_corona --source genbank --fname human_cov_annotated.fasta` + +## Download from fauna + +`python2 vdb/seasonal_corona_download.py -db vdb -v seasonal_corona --fstem seasonal_corona` diff --git a/package-lock.json b/package-lock.json index 351435a..1c82c06 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,7 +9,7 @@ "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.5.tgz", "integrity": "sha1-63d99gEXI6OxTopywIBcjoZ0a9I=", "requires": { - "mime-types": "2.1.21", + "mime-types": "~2.1.18", "negotiator": "0.6.1" } }, @@ -23,7 +23,7 @@ "resolved": "https://registry.npmjs.org/acorn-globals/-/acorn-globals-1.0.9.tgz", "integrity": "sha1-VbtemGkVB7dFedBRNBMhfDgMVM8=", "requires": { - "acorn": "2.7.0" + "acorn": "^2.1.0" } }, "align-text": { @@ -31,9 +31,9 @@ "resolved": 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+OC43/SLO/62794/2016 2016-02-05 +OC43/SLO/63863/2016 2016-02-20 +sh2606 2014-12-01 +sh2613 2014-12-01 +sh2656 2014-12-01 +sh2677 2014-12-01 +sh2678 2014-12-01 +sh2679 2014-12-01 +sh2687 2014-12-01 +sh2701 2014-12-01 +sh2702 2014-12-01 +sh2711 2014-12-01 +sh2724 2014-12-01 +sh2726 2014-12-01 +sh2731 2014-12-01 +sh2742 2014-12-01 +sh2796 2014-12-01 +sh2875 2014-12-01 +sh2928 2014-12-01 +sh2949 2014-12-01 +sh2979 2014-12-01 +sh3053 2014-12-01 +sh3060 2014-12-01 diff --git a/source-data/seasonal_corona_location_fix.tsv b/source-data/seasonal_corona_location_fix.tsv new file mode 100644 index 0000000..b9921d6 --- /dev/null +++ b/source-data/seasonal_corona_location_fix.tsv @@ -0,0 +1,2 @@ +label fix + diff --git a/source-data/seasonal_corona_strain_name_fix.tsv b/source-data/seasonal_corona_strain_name_fix.tsv new file mode 100644 index 0000000..6c7b354 --- /dev/null +++ b/source-data/seasonal_corona_strain_name_fix.tsv @@ -0,0 +1 @@ +label fix diff --git a/vdb/seasonal_corona_download.py b/vdb/seasonal_corona_download.py new file mode 100644 index 0000000..a6f850f --- /dev/null +++ b/vdb/seasonal_corona_download.py @@ -0,0 +1,21 @@ +import os,datetime +from download import download +from download import get_parser + +class seasonal_corona_download(download): + def __init__(self, **kwargs): + download.__init__(self, **kwargs) + +if __name__=="__main__": + parser = get_parser() + args = parser.parse_args() + fasta_fields = ['accession', 'strain', 'virus', 'collection_date', + 'country', 'source', 'sequence_locus', 'subtype', 'type'] + args.fasta_fields = fasta_fields + current_date = str(datetime.datetime.strftime(datetime.datetime.now(),'%Y_%m_%d')) + if args.fstem is None: + args.fstem = args.virus + '_' + current_date + if not os.path.isdir(args.path): + os.makedirs(args.path) + connfluVDB = seasonal_corona_download(**args.__dict__) + connfluVDB.download(**args.__dict__) diff --git a/vdb/seasonal_corona_upload.py b/vdb/seasonal_corona_upload.py new file mode 100644 index 0000000..ee7d78a --- /dev/null +++ b/vdb/seasonal_corona_upload.py @@ -0,0 +1,139 @@ +import os, re, time, datetime, csv, sys +import rethinkdb as r +from Bio import SeqIO +from upload import upload +from upload import get_parser +from Bio import SeqIO +from Bio.SeqRecord import SeqRecord + +def add_subtype_to_virus_fastas(): + #Append virus subtype to fasta fields, to ultimately create column in fauna + input_fasta = "data/human_cov_genome.fasta" + output_fasta = str(input_fasta.replace('.fasta',''))+"_annotated.fasta" + #subtypes to look for + cov_subtypes = ['OC43', 'HKU1', 'NL63', '229E'] + cov_types = {'OC43':'beta', 'HKU1':'beta', 'NL63':'alpha', '229E':'alpha'} + + sequences = [] + + with open(input_fasta, "r") as handle: + for record in SeqIO.parse(handle, "fasta"): + #Fasta fields format: 'gb-id|strain|segment|date|host|country|subtype|virus species' + new_record_list = record.description.split('|') + + #Annotate subtypes + new_record_list = new_record_list+['None', 'None', 'full'] + for subtype in cov_subtypes: + if subtype in record.description: + new_record_list[-3] = subtype.lower() + new_record_list[-2] = cov_types[subtype] + #New fasta fields format: 'gb-id|strain|segment|date|host|country|subtype|virus species|subtype|type|sequence_locus' + new_record_description = '|'.join(new_record_list) + + + sequences.append(SeqRecord(record.seq, id=new_record_description, description=new_record_description)) + + SeqIO.write(sequences, output_fasta, "fasta") + +def add_subtype_to_gene_fastas(): + #Add virus subtype info to Spike and HE sequence files as well + #Combine all Spike sequences into one file with virus type annotated + genes = ['spike', 'he'] + cov_subtypes = ['OC43', 'HKU1', 'NL63', '229E'] + cov_types = {'NL63':'alpha', '229E':'alpha', 'OC43':'beta', 'HKU1':'beta'} + + + for gene in genes: + sequences = [] + for virus_subtype in cov_subtypes: + input_fasta = 'data/'+virus_subtype+'_'+gene+'_genomealign.fasta' + try: + with open(input_fasta, "r") as handle: + for record in SeqIO.parse(handle, "fasta"): + #Fasta fields format: 'gb-id|strain|segment|date|host|country|subtype|virus species' + new_record_list = record.description.split('|') + + #Change accesion number and strain name to indicate gene, for fauna + new_record_list[0] = new_record_list[0]+'_'+str(gene) + new_record_list[1] = new_record_list[1]+'_'+str(gene) + + #Annotate subtypes + virus_type = cov_types[virus_subtype] + new_record_list = new_record_list+[virus_subtype.lower(), virus_type, gene] + + #New fasta fields format: 'gb-id|strain|segment|date|host|country|subtype|virus species|subtype|type|sequence_locus' + new_record_description = '|'.join(new_record_list) + + sequences.append(SeqRecord(record.seq, id=new_record_description, + description=new_record_description)) + except: + pass + + output_fasta = 'data/human_cov_'+str(gene)+"_annotated.fasta" + + SeqIO.write(sequences, output_fasta, "fasta") + + +def combine_all_loci_fastas(vipr_upload, gene_upload): +#Combine full_seq, spike, he into one fasta file for upload + if vipr_upload==False and gene_upload==False: + loci = ['genome','spike','he'] + elif vipr_upload==False and gene_upload==True: + loci = ['spike','he'] + elif vipr_upload==True and gene_upload==False: + loci = ['genome'] + + sequences = [] + for locus in loci: + input_fasta = 'data/human_cov_'+locus+'_annotated.fasta' + with open(input_fasta, "r") as handle: + for record in SeqIO.parse(handle, "fasta"): + sequences.append(record) + + output_fasta = 'data/human_cov_annotated.fasta' + + SeqIO.write(sequences, output_fasta, "fasta") + + +class seasonal_corona_upload(upload): + def __init__(self, **kwargs): + upload.__init__(self, **kwargs) + + + def fix_name(self, name): + original_name = name + try: + name = 'V' + str(int(name)) + except: + pass + return name, original_name + + def fix_casing(self, document): + for field in ['host']: + if field in document and document[field] is not None: + document[field] = self.camelcase_to_snakecase(document[field]) + + +if __name__=="__main__": + parser = get_parser() + parser.add_argument('--vipr_upload', action='store_true', help='specify whether to upload sequences downloaded from Vipr') + parser.add_argument('--gene_upload', action='store_true', help='specify whether to upload sequences Spike and HE sequences extracted from alignments') + args = parser.parse_args() + + if args.vipr_upload == True and args.gene_upload == False: + add_subtype_to_virus_fastas() + if args.gene_upload == True and args.vipr_upload == False: + add_subtype_to_gene_fastas() + if args.vipr_upload ==False and args.gene_upload ==False: + add_subtype_to_virus_fastas() + add_subtype_to_gene_fastas() + + combine_all_loci_fastas(vipr_upload = args.vipr_upload, gene_upload = args.gene_upload) + + #gb-id|strain|segment|date|host|country|subtype|virus species|subtype|type + virus_fasta_fields = {1:'strain', 3:'collection_date', 4: 'host', 5:'country', 7:'virus_species', 8:'subtype', 9:'type', 10: 'sequence_locus'} + sequence_fasta_fields = {0:'accession', 1:'strain', 8:'subtype', 9:'type', 10: 'sequence_locus'} + setattr(args, 'virus_fasta_fields', virus_fasta_fields) + setattr(args, 'sequence_fasta_fields', sequence_fasta_fields) + connVDB = seasonal_corona_upload(**args.__dict__) + connVDB.upload(**args.__dict__)