B b.@sJdZddlmZGdddejeZGdddeZd dd Zd d Zd S)zParsing TRANSFAC files.)motifsc@s.eZdZdZdddddddhZd d d d hZd S)MotifaStore 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. BFOVHPBSHCDTDRRXRARTRLN)__name__ __module__ __qualname____doc__multiple_value_keysreference_keysrr2lib/python3.7/site-packages/Bio/motifs/transfac.pyrs1rc@s eZdZdZddZddZdS)RecordzStore 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)zInitialize the class.N)version)selfrrr__init__SszRecord.__init__cCst|S)z'Turn the TRANSFAC matrix into a string.)write)rrrr__str__WszRecord.__str__N)rrrrrrrrrrrHs rTc Csi}g}d}t}x|D]}|}|s.q|dd}|d}|rft|dkrftd|dt|dkr|d} |r|ddstd|d|d kr| |_n|d kri}| dd d d ddgkrtd|d|d} xdD] } g|| <qWx|D]}|}|dd}|d}t|dkrx|d} |rx|ddsxtd|dy t|} Wntk rPYnX| dkr| dkr|rtd|n| d7} | | krtd|d|r>t|dkr td| dd| dd|ddt|dkr>td|d| dd } t| d krltd|dx*td| D]\} }||  t |qxWqW|dkrq|dkrl| d \}}}|dd!krtd"|d#|d|d$d%kr td"|d&|dt|dd$}t||dkrXtd"|dd't|ddd|dd|| i}| |q|d(kr|dk rt d|d)}| |||_ | |i}g}q|t jkr| ||<q|t jkr||krg||<|| | q| ||<qW|S)*z4Parse a transfac format handle into a Record object.NrzAThe key value of a TRANSFAC motif line should have 2 characters:""z zKA TRANSFAC motif line should have 2 spaces between key and value columns: "ZVV)P0ZPOACGTzA TRANSFAC matrix "z(" line should be followed by "A C G T": ZACGTzaA TRANSFAC matrix should start with "01" as first row of the matrix, but this matrix uses "00": "zKThe TRANSFAC matrix row number does not match the position in the matrix: "zLA TRANSFAC matrix line should have a 2 digit key at the start of the line ("Z02dz"), but this matrix uses "dz": "sz".z7A TRANSFAC matrix line should have a key and a value: "zQA TRANSFAC matrix line should have a value for each nucleotide (A, C, G and T): "XXRN;[z The index "z2" in a TRANSFAC RN line should start with a "[": "]z0" in a TRANSFAC RN line should end with a "]": "zP" of the TRANSFAC RN line does not match the current number of seen references "z//)alphabetcounts)rstripsplitlen ValueError partitionrintzipappendfloatrupdate referencesrr)ZhandlestrictZ annotationsr:r/recordline key_valuekeyvaluelengthcivaluesvindexZ separatorZ accession referencemotifrrrread\s                 (           rIc sg}y |j}Wntk r"YnX|dk r>d|}||tj}d}x&|D]g}x|D]}d}x|D]} | dkr.j} | dkrqtj} tj} d dg| } || xht | D]\d d gd d | Dd } | t d gfdd | D| g} || qWd}ny | }Wntk rVd}YnX|dk r| |krx<|D]}d| |f} || qrWnd| |f} || d}| dkrty j }Wntk rYqtXd}xP|D]H}x@|D]8} | | }|dkrqd| |f} || d}qWqWqtW|rbd} || qbWd} || d |d}||qPWd |}|S)z7Write the representation of a motif in TRANSFAC format.Nz VV %s XX // ))ZACZAS)ZID)r ZCO)ZNA)ZDE)ZTY)ZOSZOC)rr)r)r )ZBA)r)ZCC)r )rPVFr rz  z%02.dcSsg|]}dqS)z%6.20gr).0_rrr szwrite..z %srcsg|]}j|qSr)r/)rLl)rCrHrrrNsTz%s %srJ)r)r r r rr(z// )rAttributeErrorr7rrrAZdegenerate_consensussortedr.joinrangetuplegetr:)rZblocksrblockrZsectionslinesZsectionZblankr?rAZsequenceZlettersr=r@rEr:keysrGtextr)rCrHrrs     ,                rN)T) rZBiorrdictlistrrIrrrrrs  :