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

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 …

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; 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

__init__(self)

Initialize the class.

__repr__(self)

Return repr(self).

__str__(self)

Return str(self).