>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY
QAGAREGAERGLSAIRERLGPLVEQGRVRAATVGSLAGQPLQERAQAWGERLRARMEEMG
SRTRDRLDEVKEQVAEVRAKLEEQAQQIRLQAEAFQARLKSWFEPLVEDMQRQWAGLVEK
VQAAVGTSAAPVPSDNH
>P17427
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA

P02649  3   23
P02649  130 162
P17427  25  27

>P02649:3-23
VLWAALLVTFLAGCQAKVEQA
>P02649:130-162
CGRLVQYRGEVQAMLGQSTEELRVRLASHLRKL
>P17427:25-27
SKE

#!/usr/bin/python 
import sys 
import socket 
import string 
import random 
import os 
import re 
 
FASTA= sys.argv[1] 
BED= sys.argv[2] 
 
fasta= open(FASTA, 'U') 
fasta_dict= {} 
for line in fasta: 
    line= line.strip() 
    if line == '': 
        continue 
    if line.startswith('>'): 
        seqname= line.lstrip('>') 
        seqname= re.sub('\..*', '', seqname) 
        fasta_dict[seqname]= '' 
    else: 
        fasta_dict[seqname] += line 
fasta.close() 
 
bed= open(BED, 'U') 
for line in bed: 
    line= line.strip().split('\t') 
    outname= line[0] + ':' + line[1] + '-' + line[2] 
    print('>' + outname) 
    s= int(line[1]) 
    e= int(line[2]) 
    print(fasta_dict[line[0]][s:e]) 
bed.close() 
sys.exit()

Traceback (most recent call last):
  File "domainseq.py", line 29, in <module>
    outname= line[0] + ':' + line[1] + '-' + line[2]
IndexError: list index out of range