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# Copyright 2016 by Stephen Marshall. 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.
"""Parser for the cellosaurus.txt file from ExPASy.
See https://web.expasy.org/cellosaurus/
Tested with the release of Version 18 (July 2016).
Functions:
- read Reads a file containing one cell line entry
- parse Reads a file containing multiple cell line entries
Classes:
- Record Holds cell line data.
Examples
--------
You need to download the Cellosaurus database for this examples to
run, e.g. from ftp://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt
>> from Bio.ExPASy import cellosaurus
>> with open('cellosaurus.txt') as handle:
... records = cellosaurus.parse(handle)
... for record in records:
... if 'Homo sapiens' in record['OX'][0]:
... print(record['ID'])
...
#15310-LN
#W7079
(L)PC6
00136
...
"""
def parse(handle):
"""Parse cell line records.
This function is for parsing cell line files containing multiple
records.
Arguments:
- handle - handle to the file.
"""
while True:
record = __read(handle)
if not record:
break
yield record
def read(handle):
"""Read one cell line record.
This function is for parsing cell line files containing
exactly one record.
Arguments:
- handle - handle to the file.
"""
record = __read(handle)
# We should have reached the end of the record by now
remainder = handle.read()
if remainder:
raise ValueError("More than one cell line record found")
return record
class Record(dict):
"""Holds information from an ExPASy Cellosaurus record as a Python dictionary.
Each record contains the following keys:
--------- --------------------------- ----------------------
Line code Content Occurrence in an entry
--------- --------------------------- ----------------------
ID Identifier (cell line name) Once; starts an entry
AC Accession (CVCL_xxxx) Once
AS Secondary accession number(s) Optional; once
SY Synonyms Optional; once
DR Cross-references Optional; once or more
RX References identifiers Optional: once or more
WW Web pages Optional; once or more
CC Comments Optional; once or more
ST STR profile data Optional; once or more
DI Diseases Optional; once or more
OX Species of origin Once or more
HI Hierarchy Optional; once or more
OI Originate from same individual Optional; once or more
SX Sex (gender) of cell Optional; once
CA Category Once
// Terminator Once; ends an entry
"""
def __init__(self):
"""Initialize the class."""
dict.__init__(self)
self["ID"] = ""
self["AC"] = ""
self["AS"] = ""
self["SY"] = ""
self["DR"] = []
self["RX"] = []
self["WW"] = []
self["CC"] = []
self["ST"] = []
self["DI"] = []
self["OX"] = []
self["HI"] = []
self["OI"] = []
self["SX"] = ""
self["CA"] = ""
def __repr__(self):
if self["ID"]:
if self["AC"]:
return "%s (%s, %s)" % (self.__class__.__name__, self["ID"], self["AC"])
else:
return "%s (%s)" % (self.__class__.__name__, self["ID"])
else:
return "%s ( )" % (self.__class__.__name__)
def __str__(self):
output = "ID: " + self["ID"]
output += " AC: " + self["AC"]
output += " AS: " + self["AS"]
output += " SY: " + self["SY"]
output += " DR: " + repr(self["DR"])
output += " RX: " + repr(self["RX"])
output += " WW: " + repr(self["WW"])
output += " CC: " + repr(self["CC"])
output += " ST: " + repr(self["ST"])
output += " DI: " + repr(self["DI"])
output += " OX: " + repr(self["OX"])
output += " HI: " + repr(self["HI"])
output += " OI: " + repr(self["OI"])
output += " SX: " + self["SX"]
output += " CA: " + self["CA"]
return output
# Everything below is private
def __read(handle):
record = None
for line in handle:
key, value = line[:2], line[5:].rstrip()
if key == "ID":
record = Record()
record["ID"] = value
elif key in ["AC", "AS", "SY", "SX", "CA"]:
record[key] += value
elif key in [
"AC",
"AS",
"SY",
"RX",
"WW",
"CC",
"ST",
"DI",
"OX",
"HI",
"OI",
"SX",
"CA",
]:
record[key].append(value)
elif key == "DR":
k, v = value.split(";")
record["DR"].append((k.strip(), v.strip()))
elif key == "//":
if record:
return record
else:
continue
if record:
raise ValueError("Unexpected end of stream")
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