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#!/usr/bin/python3
import sys
import re
import textwrap
import argparse
import MySQLdb.cursors
db = MySQLdb.connect(db='uniprot', host='wrpxdb.bioch.virginia.edu', user='web_user', passwd='fasta_www',
cursorclass=MySQLdb.cursors.DictCursor)
cur1 = db.cursor()
cur2 = db.cursor()
get_iso_acc='select acc from annot2_iso where prim_acc="%s"'
get_fasta_info='select db, acc, id, descr, seq from annot2 join protein using(acc) where acc="%s"'
get_iso_fasta_info='select db, acc, id, descr, seq from annot2_iso join protein_iso using(acc) where prim_acc="%s"'
fasta_seqs=[]
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]
cur1.execute(get_fasta_info%(acc,))
row = cur1.fetchone()
if (row):
fasta_seqs.append(row)
else:
sys.stderr.write("***error*** %s sequence not found\n"%(acc))
continue
cur2.execute(get_iso_fasta_info%(acc,))
for row in cur2:
fasta_seqs.append(row)
for row in fasta_seqs:
print(">%s|%s|%s %s"%(row['db'],row['acc'],row['id'],row['descr']))
print('\n'.join(textwrap.wrap(row['seq'])))
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