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 …
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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.
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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.
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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
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__init__
(self)¶ Initialize the class.
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__repr__
(self)¶ Return repr(self).
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__str__
(self)¶ Return str(self).
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