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#!/usr/bin/env python
# Copyright 2000 Thomas Hamelryck. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Example indexing plain text SwissProt files.
Example code to index a non-reduntant protein database of
SwissProt + TrEMBL for fast lookup and retrieval.
To build the database and index it::
cd /opt/bio/data/
wget -N -nd -r -l1 -A'.dat.Z' ftp://expasy.cbr.nrc.ca/databases/sp_tr_nrdb/
zcat *.dat.Z > nr.dat
./getgene.py --index nr.dat
setenv PYPHY '/opt/bio/data'
To retrieve entries from the command line::
./getgene.py EFTU_ECOLI
To use from a python script::
from getgene import DB_Index
db_index = DB_Index()
# retrieve a complete entry:
db_index.Get('EFTU_ECOLI')
# get organism, lineage and gene
db_index.Get_OS_OC_GN('EFTU_ECOLI')
"""
import os
import re
import string
import sys
from dbm import gnu as gdbm
class DB_Index:
"""A class to index a SwissProt/TrEMBL database file for fast retrieval."""
def __init__(self, open=True):
"""Initialise.
Optional argument open controls if the index should be opened.
"""
if open:
self.Open()
def Create(self, infile, outfile):
"""Build the database from file."""
db = gdbm.open(outfile, "n")
with open(infile) as fid:
db["datafile"] = os.path.abspath(infile)
while True:
line = fid.readline()
if not line or not len(line):
break
if line[:3] == "ID ":
id = string.split(line)[1]
start = fid.tell() - len(line)
elif line[:3] == "AC ":
acc = string.split(line)[1]
if acc[-1] == ";":
acc = acc[:-1]
elif line[:2] == "//":
stop = fid.tell()
try:
value = "%d %d" % (start, stop)
db[id] = value
db[acc] = value
id, acc, start, stop = None, None, None, None
except Exception:
print(
"AARRGGGG %d %d %s %s"
% (start, stop, type(start), type(stop))
)
print("%s %s" % (id, acc))
db.close()
def Open(self, indexfile=None):
"""Open the indexed database file."""
if not indexfile:
indexfile = os.path.join(os.environ["PYPHY"], "nr.dat.indexed")
self.db = gdbm.open(indexfile)
self.datafile = self.db["datafile"]
self.fid = open(self.datafile)
def Close(self):
"""Close the database."""
self.db.close()
def Get(self, id):
"""Retrieve complete entry for given id."""
try:
values = self.db[id]
except Exception:
return None
start, stop = [int(x) for x in values.split()]
self.fid.seek(start)
txt = self.fid.read(stop - start)
return txt
def Get_Organism(self, id):
"""Retrieve the organism species (OS)."""
entry = self.Get(id)
if not entry:
return None
for line in string.split(entry, "\n"):
if line[0:5] == "OS ":
OS = string.strip(line[5:])
if OS[-1] == ".":
OS = OS[0:-1]
return OS
if line[0:2] == "//":
break
return None
def FixOS(self, os):
"""Extract species from organism species field (OS)."""
os = string.split(os, ",")[0]
os = string.split(os, "(")[0]
return string.strip(os)
def Get_Taxonomy(self, id):
"""Retrieve the organism classification (OC)."""
entry = self.Get(id)
if not entry:
return None
OC = ""
for line in string.split(entry, "\n"):
if line[0:5] == "OC ":
OC = OC + string.strip(line[5:])
if OC[-1] == ".":
OC = OC[0:-1]
if line[0:2] == "//":
break
return OC
def Get_Kingdom(self, id):
"""Retrieve kingdom from OC field and return as single letter code."""
res = self.Get_Taxonomy(id)
# print("%s %s" % (id, res))
if not res:
return "U"
kd = string.strip(string.split(res, ";")[0])
if kd == "Eubacteria" or kd == "Prokaryota" or kd == "Bacteria":
return "B"
elif kd == "Eukaryota" or kd == "Eukaryotae":
return "E"
elif kd == "Archaebacteria" or kd == "Archaea":
return "A"
elif kd == "Viridae" or kd == "Viruses":
return "V"
else:
print("%s UNKNOWN" % kd)
return "U"
def Get_Gene(self, id):
"""Retreive the gene name (GN)."""
entry = self.Get(id)
if not entry:
return None
GN = ""
for line in string.split(entry, "\n"):
if line[0:5] == "GN ":
GN = string.strip(line[5:])
if GN[-1] == ".":
GN = GN[0:-1]
return GN
if line[0:2] == "//":
break
return GN
def Get_OS_OC_GN(self, id):
"""Retrieve organism species + classification and gene name."""
entry = self.Get(id)
if not entry:
return None, None, None
OS, OC, GN = "", "", ""
for line in string.split(entry, "\n"):
if line[0:5] == "OS ":
OS = string.strip(line[5:])
if OS[-1] == ".":
OS = OS[0:-1]
if line[0:5] == "OC ":
OC = OC + string.strip(line[5:])
if OC[-1] == ".":
OC = OC[0:-1]
if line[0:5] == "GN ":
GN = string.strip(line[5:])
if GN[-1] == ".":
GN = GN[0:-1]
if line[0:2] == "//":
break
return OS, OC, GN
def Get_OS_OC_OG(self, id):
"""Retreive organism species + classification and organelle."""
entry = self.Get(id)
if not entry:
return None, None, None
OS, OC, OG = "", "", ""
for line in string.split(entry, "\n"):
if line[0:5] == "OS ":
OS = string.strip(line[5:])
if OS[-1] == ".":
OS = OS[0:-1]
if line[0:5] == "OC ":
OC = OC + string.strip(line[5:])
if OC[-1] == ".":
OC = OC[0:-1]
if line[0:5] == "OG ":
OG = string.strip(line[5:])
if OG[-1] == ".":
OG = OG[0:-1]
if line[0:2] == "//":
break
return OS, OC, OG
def Get_SQ(self, id, fasta=1):
"""Retrieve sequence."""
entry = self.Get(id)
if not entry:
return ""
SQ = ""
record = 0
for line in string.split(entry, "\n"):
if record:
SQ = SQ + string.strip(line[5:])
if line[0:5] == "SQ ":
record = 1
if line[0:2] == "//":
break
SQ = re.sub("[ \n]", "", SQ)
if fasta:
SQ = ">%s\n%s" % (id, re.sub("(.{60})", "\\1\n", SQ))
return SQ
def Get_XX(self, id, xx):
"""Retrieve the information with a given line code (e.g. ID, AC)."""
entry = self.Get(id)
if not entry:
return ""
XX = ""
for line in string.split(entry, "\n"):
if line[0:5] == "%s " % xx:
XX = XX + string.strip(line[5:])
if XX[-1] == ".":
XX = XX[0:-1]
if line[0:2] == "//":
break
return XX
def Get_Keywords(self, id):
"""Retrieve the keywords (KW)."""
entry = self.Get(id)
if not entry:
return []
keywords = []
for line in string.split(entry, "\n"):
if line[0:5] == "KW ":
for i in string.split(string.strip(line[5:]), ";"):
kw = string.strip(i)
if len(kw) < 2:
continue
if kw[-1] == ".":
kw = kw[:-1]
keywords.append(kw)
if line[0:2] == "//":
break
return keywords
def usage(exit=0):
"""Print a short help message."""
name = os.path.basename(sys.argv[0])
print("Usage: %s <db> <gene ID>" % name)
print(" or %s --index <db.dat>" % name)
if exit:
sys.exit(0)
if __name__ == "__main__":
pyphy_home = os.environ.get("PYPHY")
if len(sys.argv) == 1:
usage(exit=1)
db_index = DB_Index(open=0)
func = db_index.Get
for arg in sys.argv[1:]:
if arg == "--index":
sys.argv.remove(arg)
infile = sys.argv[1]
outfile = os.path.basename(infile) + ".indexed"
db_index.Create(infile, outfile)
sys.exit(0)
elif arg[:4] == "-Get":
sys.argv.remove(arg)
func = getattr(db_index, arg[1:])
elif arg == "-h" or arg == "--help":
usage(exit=1)
db = "nr.dat"
if len(sys.argv) == 2:
# shortcut, mostly we use nr.dat so dont bother to name it
ids = sys.argv[1:]
else:
try:
db = sys.argv[1]
ids = sys.argv[2:]
except Exception:
usage(exit=1)
dbfile = os.path.join(pyphy_home, db + ".indexed")
db_index.Open(dbfile)
for id in ids:
# print(db_index.Get(id))
print(func(id))
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