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#!/usr/bin/python3
## get_protein.py --
## get a protein sequence from Uniprot or NCBI/Refseq using the accession
##
import sys
import re
import textwrap
import MySQLdb
import time
from urllib.request import Request, urlopen
from urllib.error import URLError
ncbi_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
uniprot_url = "https://www.uniprot.org/uniprot/"
(host, user, passwd, db) = ("wrpxdb.its.virginia.edu","web_user","fasta_www","seqdb_demo2")
db = MySQLdb.connect(host,user,passwd,db)
cur = db.cursor()
get_refseq_sql = '''select acc, descr, seq from annot join protein using(prot_id) where acc="%s"'''
get_up_sql = '''select db, acc, id, descr, seq from uniprot.annot2 join uniprot.protein using(acc) where acc="%s"'''
get_up_iso_sql = '''select db, acc, id, descr, seq from uniprot.annot2_iso join uniprot.protein_iso using(acc) where acc="%s"'''
def get_ncbi_sql(acc, cur):
result = cur.execute(get_refseq_sql%(acc,))
if (result):
acc, descr, seq = cur.fetchone()
seq = re.sub(r'(.{60})',r'\g<1>\n',seq)
return ">%s %s\n%s\n"%(acc, descr, seq)
else:
return False
def get_ncbi_www(acc):
db_type="protein"
seq_args = "db=%s&id=" % (db_type) + acc + "&rettype=fasta"
## seq_html = urlopen(ncbi_url + seq_args)
req = Request(ncbi_url+seq_args)
try:
resp = urlopen(req)
except URLError as e:
seq_html = ''
if hasattr(e, 'reason'):
sys.stderr.write("Sequence [%s] not found: %s\n"%(acc,str(e.reason)))
elif hasattr(e, 'code'):
sys.stderr.write("Sequence [%s] not found: %s\n"%(acc,str(e.ecode)))
else:
sys.stderr.write("Sequence [%s] not found\n"%(acc))
exit(0)
else:
seq_html=resp.read().decode('utf-8')
time.sleep(0.3)
return seq_html
def get_uniprot_sql(acc, cur):
result = cur.execute(get_up_sql%(acc,))
if (not result):
result = cur.execute(get_up_iso_sql%(acc,))
if (result):
db, acc, id, descr, seq = cur.fetchone()
# not needed because of final textwrap
# seq = re.sub(r'(.{60})',r'\g<1>\n',seq)
return ">%s|%s|%s %s\n%s\n"%(db, acc, id, descr, seq)
else:
return False
def get_uniprot_www(acc):
seq_html = urlopen(uniprot_url + acc + ".fasta").read().decode('utf-8')
return seq_html
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'[NXYW]P_',acc)):
seq_html = get_ncbi_sql(acc,cur)
if (not seq_html):
seq_html = get_ncbi_www(acc)
else:
seq_html = get_uniprot_sql(acc,cur)
if (not seq_html):
seq_html = get_uniprot_www(acc)
if not seq_html:
continue;
header=''
seq = ''
for line in seq_html.split('\n'):
if (line and line[0]=='>'):
# print out old one if there
if (header):
if (sub_range):
start, stop = sub_range.split('-')
start, stop = int(start), int(stop)
if (start > 0):
start -= 1
new_seq = seq[start:stop]
else:
start = 0
new_seq = seq
if (start > 0):
print("%s @C%d" %(header, start+1))
else:
print(header)
print('\n'.join(textwrap.wrap(new_seq)))
header = line;
seq = ''
else:
seq += line
start=0
if (sub_range):
start, stop = sub_range.split('-')
start, stop = int(start), int(stop)
if (start > 0):
start -= 1
new_seq = seq[start:stop]
else:
new_seq = seq
if (start > 0):
print("%s @C:%d" %(header, start+1))
else:
print(header)
print('\n'.join(textwrap.wrap(new_seq)))
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