:>"^ä/ã@sgdZddlmZGdd„dejeƒZGdd„deƒZddd „Zd d „Zd S) zParsing TRANSFAC files.é)Úmotifsc@sCeZdZdZdddddddhZd d d d hZd S)ÚMotifaŠStore the information for one TRANSFAC motif. This class inherits from the Bio.motifs.Motif base class, as well as from a Python dictionary. All motif information found by the parser is stored as attributes of the base class when possible; see the Bio.motifs.Motif base class for a description of these attributes. All other information associated with the motif is stored as (key, value) pairs in the dictionary, where the key is the two-letter fields as found in the TRANSFAC file. References are an exception: These are stored in the .references attribute. These fields are commonly found in TRANSFAC files:: AC: Accession number AS: Accession numbers, secondary BA: Statistical basis BF: Binding factors BS: Factor binding sites underlying the matrix [sequence; SITE accession number; start position for matrix sequence; length of sequence used; number of gaps inserted; strand orientation.] CC: Comments CO: Copyright notice DE: Short factor description DR: External databases [database name: database accession number] DT: Date created/updated HC: Subfamilies HP: Superfamilies ID: Identifier NA: Name of the binding factor OC: Taxonomic classification OS: Species/Taxon OV: Older version PV: Preferred version TY: Type XX: Empty line; these are not stored in the Record. References are stored in an .references attribute, which is a list of dictionaries with the following keys:: RN: Reference number RA: Reference authors RL: Reference data RT: Reference title RX: PubMed ID For more information, see the TRANSFAC documentation. ÚBFÚOVÚHPÚBSÚHCÚDTÚDRÚRXÚRAÚRTÚRLN)Ú__name__Ú __module__Ú __qualname__Ú__doc__Úmultiple_value_keysÚreference_keys©rrú8/tmp/pip-build-ww9dw3qa/biopython/Bio/motifs/transfac.pyr s 1rc@s.eZdZdZdd„Zdd„ZdS)ÚRecordzñStore the information in a TRANSFAC matrix table. The record inherits from a list containing the individual motifs. Attributes: - version - The version number, corresponding to the 'VV' field in the TRANSFAC file; cCs d|_dS)z Initialize.N)Úversion)ÚselfrrrÚ__init__QszRecord.__init__cCs t|ƒS)z'Turn the TRANSFAC matrix into a string.)Úwrite)rrrrÚ__str__UszRecord.__str__N)rrrrrrrrrrrFs  rTcCsþi}g}d}tƒ}xÜ|D]Ô}|jƒ}|s=q"|jddƒ}|djƒ}|rŒt|ƒdkrŒtdj|ƒƒ‚t|ƒdkrÜ|djƒ} |rÜ|jdƒdsÜtdj|ƒƒ‚|dkrô| |_nT|d"krHi}| jƒdd …d d ddgkrFtdj||ƒƒ‚d} xdD]} g|| s zwrite..z %srcs!g|]}ˆj|ˆ‘qSr)r,)rYrZ)rDrJrrr[s Tz%s %sr'r r r rr&z//Ú Ú©rLrM©rN©zDTrO©rP©rQ©rR©rSrT©zHPzHC©zBF©zP0©rU©zBS©zCC©zDR©zOVrW)r^r_r`rarbrcrdrerfrgrhrirjrkrl)zRNzRXzRAzRTzRL)rÚAttributeErrorr6rrrBZdegenerate_consensusÚsortedr+ÚjoinÚrangeÚtupleÚgetr9)rÚblocksrÚblockrÚsectionsÚlinesÚsectionZblankr@rBÚsequenceÚlettersr>rArFr9ÚkeysrIÚtextr)rDrJrrÐs¤              $               rN) rZBiorrÚdictÚlistrrKrrrrrÚs :v