# 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.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 85
  __static_attributes__ = ()

Biopython v: 1.86

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