B ‰°bÞã@s0dZdd„Zdd„ZGdd„deƒZdd„Zd S) a)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 ... ccsxt|ƒ}|sP|VqWdS)z§Parse cell line records. This function is for parsing cell line files containing multiple records. Arguments: - handle - handle to the file. N)Ú__read)ÚhandleÚrecord©rú5lib/python3.7/site-packages/Bio/ExPASy/cellosaurus.pyÚparse(s rcCs t|ƒ}| ¡}|rtdƒ‚|S)z«Read one cell line record. This function is for parsing cell line files containing exactly one record. Arguments: - handle - handle to the file. z$More than one cell line record found)rÚreadÚ ValueError)rrZ remainderrrrr9s rc@s(eZdZdZdd„Zdd„Zdd„ZdS) ÚRecorda{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 cCs†t |¡d|d<d|d<d|d<d|d<g|d<g|d<g|d<g|d <g|d <g|d <g|d <g|d <g|d<d|d<d|d<dS)zInitialize the class.ÚÚIDÚACÚASÚSYÚDRÚRXÚWWÚCCÚSTÚDIÚOXÚHIÚOIÚSXÚCAN)ÚdictÚ__init__)Úselfrrrrfs  zRecord.__init__cCsP|dr@|dr*d|jj|d|dfSd|jj|dfSn d|jjSdS)Nr r z %s (%s, %s)z%s (%s)z%s ( ))Ú __class__Ú__name__)rrrrÚ__repr__ys zRecord.__repr__cCsd|d}|d|d7}|d|d7}|d|d7}|d t|d ƒ7}|d t|d ƒ7}|d t|dƒ7}|dt|dƒ7}|dt|dƒ7}|dt|dƒ7}|dt|dƒ7}|dt|dƒ7}|dt|dƒ7}|d|d7}|d|d7}|S)NzID: r z AC: r z AS: r z SY: rz DR: rz RX: rz WW: rz CC: rz ST: rz DI: rz OX: rz HI: rz OI: rz SX: rz CA: r)Úrepr)rÚoutputrrrÚ__str__‚s  zRecord.__str__N)rÚ __module__Ú __qualname__Ú__doc__rrr"rrrrr Ks r cCsÎd}x¸|D]°}|dd…|dd… ¡}}|dkrDtƒ}||d<q |dkr^|||7<q |dkrv|| |¡q |dkr¨| d¡\}}|d | ¡| ¡f¡q |dkr |r |Sq q W|rÊtd ƒ‚dS) Néér )r r rrr) r r rrrrrrrrrrrrú;z//zUnexpected end of stream)Úrstripr ÚappendÚsplitÚstripr)rrÚlineÚkeyÚvalueÚkÚvrrrr˜s&  rN)r%rrrr rrrrrÚ%sM