Mercurial > repos > iuc > data_manager_snpsift_dbnsfp
view data_manager/data_manager_snpsift_dbnsfp.py @ 0:0e9e3bb5776a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
author | iuc |
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date | Tue, 07 Jun 2016 10:23:16 -0400 |
parents | |
children | 3d4cd0e3891f |
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#!/usr/bin/env python import gzip import json import optparse import os import os.path import re import shutil import sys import urllib import zipfile from pysam import ctabix """ # Install dbNSFP databases # from DbNsfp site # Download dbNSFP database $ wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv2.4.zip # Uncompress $ unzip dbNSFP2.4.zip # Create a single file version $ (head -n 1 dbNSFP2.4_variant.chr1 ; cat dbNSFP2.4_variant.chr* | grep -v "^#") > dbNSFP2.4.txt # Compress using block-gzip algorithm bgzip dbNSFP2.4.txt # Create tabix index tabix -s 1 -b 2 -e 2 dbNSFP2.4.txt.gz data_table: <table name="snpsift_dbnsfps" comment_char="#"> <columns>key, build, name, value, annotations</columns> <file path="tool-data/snpsift_dbnsfps.loc" /> </table> #id build description path annotations #GRCh37_dbNSFP2.4 GRCh37 GRCh37 dbNSFP2.4 /depot/snpeff/dbNSFP2.4.gz SIFT_pred,Uniprot_acc #GRCh38_dbNSFP2.7 GRCh38 GRCh38 dbNSFP2.7 /depot/snpeff/dbNSFP2.7.gz SIFT_pred,Uniprot_acc """ data_table = 'snpsift_dbnsfps' softgenetics_url = 'ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/' dbNSFP_file_pat = '(dbNSFP(.*)_variant|dbscSNV(.*)).chr(.*)' tokenize = re.compile(r'(\d+)|(\D+)').findall dbNSFP_name_pat = 'dbNSFP(v|_light)?(\d*).*?' def stop_err(msg): sys.stderr.write(msg) sys.exit(1) def get_nsfp_genome_version(name): genome_version = 'hg19' dbNSFP_name_pat = '(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' m = re.match(dbNSFP_name_pat, name) if m: (base, mid, ver) = m.groups() if base == 'dbscSNV': genome_version = 'hg19' else: genome_version = 'hg38' if ver == '3' else 'hg19' if ver == '2' else 'hg18' return genome_version def get_annotations(gzip_path): annotations = None fh = None try: fh = gzip.open(gzip_path, 'r') buf = fh.read(10000) lines = buf.splitlines() headers = lines[0].split('\t') annotations = ','.join([x.strip() for x in headers[4:]]) except Exception as e: stop_err('Error Reading annotations %s : %s' % (gzip_path, e)) finally: if fh: fh.close() return annotations def tabix_file(input_fname, output_fname): print >> sys.stdout, "tabix_file: %s -> %s" % (input_fname, output_fname) ctabix.tabix_compress(input_fname, output_fname, force=True) # Column indices are 0-based. ctabix.tabix_index(output_fname, seq_col=0, start_col=1, end_col=1) def natural_sortkey(string): return tuple(int(num) if num else alpha for num, alpha in tokenize(string)) def download_dbnsfp_database(url, output_file): dbnsfp_tsv = None file_path = 'downloaded_file' urllib.urlretrieve(url, file_path) with zipfile.ZipFile(file_path, 'r') as my_zip: dbnsfp_tsv = output_file if output_file else 'dbnsfp_tsv' wtr = open(dbnsfp_tsv, 'w') allfiles = [info.filename for info in my_zip.infolist()] files = [f for f in allfiles if re.match(dbNSFP_file_pat, f)] files = sorted(files, key=natural_sortkey) for j, file in enumerate(files): fh = my_zip.open(file, 'rU') for i, line in enumerate(fh): if j > 0 and i == 0: continue wtr.write(line) return dbnsfp_tsv def main(): # Parse Command Line parser = optparse.OptionParser() parser.add_option('-g', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='dbkey genome version') parser.add_option('-n', '--db_name', dest='db_name', action='store', type="string", default=None, help='A name for a history snpsiftdbnsfp dataset') parser.add_option('-s', '--softgenetics', dest='softgenetics', action='store', type="string", default=None, help='A name for softgenetics dbNSFP file') parser.add_option('-H', '--snpsiftdbnsfp', dest='snpsiftdbnsfp', action='store', type="string", default=None, help='A history snpsiftdbnsfp dataset') parser.add_option('-T', '--dbnsfp_tabular', dest='dbnsfp_tabular', action='store', type="string", default=None, help='A history dbnsfp_tabular dataset') (options, args) = parser.parse_args() filename = args[0] params = json.loads(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path'] if not os.path.exists(target_directory): os.mkdir(target_directory) data_manager_dict = {} genome_version = options.dbkey if options.dbkey else 'unknown' dbnsfp_tsv = None db_name = None bzip_path = None if options.softgenetics: dbnsfp_url = softgenetics_url + options.softgenetics db_name = options.db_name if options.db_name else re.sub('\.zip$', '', options.softgenetics) genome_version = get_nsfp_genome_version(options.softgenetics) tsv = db_name + '.tsv' dbnsfp_tsv = download_dbnsfp_database(dbnsfp_url, tsv) elif options.dbnsfp_tabular: db_name = options.db_name dbnsfp_tsv = options.dbnsfp_tabular elif options.snpsiftdbnsfp: (dirpath, bgzip_name) = os.path.split(options.snpsiftdbnsfp) idxpath = options.snpsiftdbnsfp + '.tbi' shutil.copy(options.snpsiftdbnsfp, target_directory) shutil.copy(idxpath, target_directory) bzip_path = os.path.join(target_directory, bgzip_name) db_name = re.sub('(.txt)?.gz$', '', bgzip_name) else: stop_err('Either --softgenetics or --dbnsfp_tabular required') if dbnsfp_tsv: bgzip_name = '%s.txt.gz' % db_name bzip_path = os.path.join(target_directory, bgzip_name) tabix_file(dbnsfp_tsv, bzip_path) annotations = get_annotations(bzip_path) # Create the SnpSift dbNSFP Reference Data data_table_entry = dict(key='%s_%s' % (genome_version, db_name), build=genome_version, name='%s %s' % (genome_version, db_name), value=bgzip_name, annotations=annotations) data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, []) data_manager_dict['data_tables'][data_table].append(data_table_entry) # save info to json file open(filename, 'wb').write(json.dumps(data_manager_dict)) if __name__ == "__main__": main()