#! /usr/bin/env python
import sys, os
import time
from Bio import Fasta
DEFAULT_DICT_FILE = '/project1/structure/mliang/pdb/derived_data/pdb_seqres.idx'
DEFAULT_OUTFH = sys.stdout
dict_file = DEFAULT_DICT_FILE
outfh = DEFAULT_OUTFH
start_time = time.time()
fdict = Fasta.Dictionary(dict_file)
elapse_time = time.time() - start_time
print >> sys.stderr, "Time to load dictionary:", elapse_time
start_time = time.time()
chainmap = {}
for key in fdict.keys():
chainmap.setdefault(key[:4], []).append(key)
elapse_time = time.time() - start_time
print >> sys.stderr, "Time to build chain map:", elapse_time
start_time = time.time()
args = sys.argv[1:]
if not args:
args = sys.stdin
for field in args:
fields = field.strip().split()
# Note that the alphabet is explicitly defined for the sequences.
import os
from Bio import Fasta
from Bio.Alphabet import IUPAC
def get_accession_num(fasta_record):
title_atoms = fasta_record.title.split()
accession_atoms = title_atoms[0].split('|')
gb_name = accession_atoms[3]
# strip the version info before returning
return gb_name[:-2]
if not os.path.isdir("my_orchid_dict.idx"):
#Build a new index
Fasta.index_file("ls_orchid.fasta", "my_orchid_dict.idx",
get_accession_num)
else:
print "Reusing existing index"
dna_parser = Fasta.SequenceParser(IUPAC.ambiguous_dna)
orchid_dict = Fasta.Dictionary("my_orchid_dict.idx", dna_parser)
for id_num in orchid_dict.keys():
print 'id number:', id_num
print 'description:', orchid_dict[id_num].description
print 'sequence:', orchid_dict[id_num].seq
