20_hgnc_name_resolution_table.py

#! /usr/bin/python3
#
# This source code is part of icgc, an ICGC processing pipeline.
# 
# Icgc is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# Icgc is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program. If not, see<http://www.gnu.org/licenses/>.
# 
# Contact: ivana.mihalek@gmail.com
#

# from HUGO gene nomenclature committee
# https://www.genenames.org/download/custom/

# header names:
# head -n1 /data/hgnc/hgnc_name_res.tsv \
# | sed 's/\t/\n/g' | awk 'ct +=1 {printf "%d ", ct; print}'

# locus group:
# | protein-coding gene |
# | non-coding RNA      |
# | pseudogene          |
# | other               |
# | phenotype           |

from config import Config
from icgc_utils.mysql import *


#########################################
def make_hgnc_table(cursor, db_name, hgnc_table, header_names):

    if check_table_exists (cursor, db_name, hgnc_table): return
    switch_to_db (cursor, db_name)

    qry = ""
    qry += "  CREATE TABLE  %s (" % hgnc_table
    qry += "     id INT NOT NULL, "
    for name in header_names:
        if name in ['approved_name', 'synonyms', 'refseq_ids']:
            charlen = 150
        elif name == 'uniprot_id_by_uniprot':
            charlen = 300
        elif name in ['approved_symbol', 'chromosome']: # chrom can have annotation such as "not on reference assembly"
            charlen = 30
        else:
            charlen = 20
        qry += " %s VARCHAR(%d)," % (name, charlen)

    qry += "	 PRIMARY KEY (id) "
    qry += ") ENGINE=MyISAM"

    rows = search_db(cursor, qry)
    print(qry)
    print(rows)
    return

#########################################
def strip_arm_annotation(chrom_address):
    if "p" in chrom_address:
        return chrom_address.split("p")[0]
    if "q" in chrom_address:
        return chrom_address.split("q")[0]
    return chrom_address

#########################################
#########################################
def main():

    hgncfile = "/storage/databases/hgnc/hgnc_name_res.tsv"

    tmp_outfile = "hgnctmp.tsv"
    ct = 0
    outf = open (tmp_outfile, "w")
    with open(hgncfile, "r") as inf:
        headers = inf.readline().rstrip("\n").split("\t")
        chromosome_column = headers.index('Chromosome')
        for line in inf:
            fields = line.rstrip("\n").split("\t")
            fields[chromosome_column] = strip_arm_annotation(fields[chromosome_column])
            ct += 1
            outfields = [str(ct)] + fields
            outf.write("\t".join(outfields)+"\n")
    outf.close()

    db     = connect_to_mysql(Config.mysql_conf_file)
    cursor = db.cursor()

    qry = "SET GLOBAL local_infile=1"
    error_intolerant_search(cursor, qry)

    db_name = "identifier_maps"
    new_headers = ["_".join(h.lower().replace("(supplied", "").replace(")", "").split(" ")) for h in headers]
    make_hgnc_table(cursor, db_name, "hgnc", new_headers)
    qry = "load data local infile '%s' into table %s" % ("hgnctmp.tsv","hgnc")
    search_db(cursor,qry,verbose=True)
    os.remove(tmp_outfile)

    cursor.close()
    db.close()

#########################################
if __name__ == '__main__':
    main()