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#!/usr/bin/python3
## get_protein_sql.py --
## get a protein sequence from a local Uniprot or NCBI/Refseq mySQL database using the accession
##
## modified to work with mysql.connector 7-Nov-2022
import sys
import re
import textwrap
import mysql.connector
db_r = mysql.connector.connect(db='seqdb_demox', host='wrpxdb.bioch.virginia.edu', user='web_user', passwd='fasta_www')
db_u = mysql.connector.connect(db='uniprot', host='wrpxdb.bioch.virginia.edu', user='web_user', passwd='fasta_www')
cur1_r = db_r.cursor(dictionary=True, buffered=True)
cur1_u = db_u.cursor(dictionary=True, buffered=True)
sql_get_uniprot='select db, acc, id, descr, seq from annot2 join protein using(acc) where acc="%s"'
sql_get_refseq ='select db, acc, "" as id, descr, seq from seqdb_demox.annot join seqdb_demox.protein using(prot_id) where acc="%s"'
sub_range = ''
for acc in sys.argv[1:]:
if (re.search(r':',acc)):
(acc, sub_range) = acc.split(':')
if (re.match(r'^(sp|tr|iso|ref)\|',acc)):
acc=acc.split('|')[1]
if (re.match(r'[A-Z]P_\d+',acc)):
sql_get_prot=sql_get_refseq
cur1 = cur1_r
else:
sql_get_prot=sql_get_uniprot
cur1 = cur1_u
cur1.execute(sql_get_prot%(acc,))
row = cur1.fetchone()
if (not row):
sys.stderr.write("*** %s *** not found\n"%(acc))
exit(1)
header = ">%s|%s"%(row['db'],row['acc'])
if (row['id']):
header += "|%s"%(row['id'])
header += " "+row['descr']
start = 0
if (sub_range):
start, stop = sub_range.split('-')
start, stop = int(start), int(stop)
if (start > 0):
seq = row['seq'][start-1:stop]
print("%s @C%d" %(header, start+1))
else:
seq = row['seq']
print(header)
print('\n'.join(textwrap.wrap(seq)))
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