Bio.ExPASy.cellosaurus module

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

This example downloads the Cellosaurus database and parses it. Note that urlopen returns a stream of bytes, while the parser expects a stream of plain string, so we use TextIOWrapper to convert bytes to string using the UTF-8 encoding. This is not needed if you download the cellosaurus.txt file in advance and open it (see the comment below).

>>> from urllib.request import urlopen
>>> from io import TextIOWrapper
>>> from Bio.ExPASy import cellosaurus
>>> url = "ftp://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt"
>>> bytestream = urlopen(url)
>>> textstream = TextIOWrapper(bytestream, "UTF-8")
>>> # alternatively, use
>>> # textstream = open("cellosaurus.txt")
>>> # if you downloaded the cellosaurus.txt file in advance.
>>> records = cellosaurus.parse(textstream)
>>> for record in records:
...     if 'Homo sapiens' in record['OX'][0]:
...         print(record['ID'])  
...
#15310-LN
#W7079
(L)PC6
0.5alpha
...

Bio.ExPASy.cellosaurus.parse(handle)

Parse cell line records.

This function is for parsing cell line files containing multiple records.

Arguments:

• handle - handle to the file.

Bio.ExPASy.cellosaurus.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.

class Bio.ExPASy.cellosaurus.Record

Bases: 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; twice 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 of cell	Optional; once
AG	Age of donor at sampling	Optional; once
CA	Category	Once
DT	Date (entry history)	Once
//	Terminator	Once; ends an entry

__init__()

Initialize the class.

__repr__()

Return the canonical string representation of the Record object.

__str__()

Return a readable string representation of the Record object.