o Rŀg_/@sJdZddlmZGdddejeZGdddeZd dd Zd d Zd S)zParsing TRANSFAC files.)motifscs0eZdZdZhdZhdZfddZZS)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. >BFBSCCDRDTHCHPOV>RARLRTRXcs:z t|}W|Styttj||}Y|Sw)N)super __getitem__ TypeErrorrr)selfkeyvalue __class__G/var/www/html/myenv/lib/python3.10/site-packages/Bio/motifs/transfac.pyrFs zMotif.__getitem__)__name__ __module__ __qualname____doc__multiple_value_keysreference_keysr __classcell__rrrrr s 2rc@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)versionrrrr__init__Ys zRecord.__init__cCst|S)z'Turn the TRANSFAC matrix into a string.)writer#rrr__str__]szRecord.__str__N)rrrrr$r&rrrrr!Ns r!Tc Csi}g}d}t}|D]}|}|sq |dd}|d}|r1t|dkr1td|dt|dkrN|d} |rN|ddsNtd|d|d krV| |_n|d vr7i}| dd gd krstd |d|d} dD]} g|| <qw|D]}|}|dd}|d}t|dkr|d} |r|ddstd|dzt|} Wn tyYnxw| dkr| dkr|rtd|n| d7} | | krtd|d|r t|dkrtd| dd| dd|ddt|dkr td|d| dd } t| d kr"td|dtd| D]\} }||  t |q'q|dkr=q |dkr| d\}}}|ddkr\td|d |d|d!d"krntd|d#|dt|dd!}t||dkrtd|dd$t|ddd|dd|| i}| |q |d%kr|durt d|d&}| |||_ | |i}g}q |t jvr| ||<q |t jvr||vrg||<|| | q | ||<q |S)'z4Parse a transfac format handle into a Record object.NrzAThe key value of a TRANSFAC motif line should have 2 characters:"" zKA TRANSFAC motif line should have 2 spaces between key and value columns: "VV)P0PO)ACGTzA TRANSFAC matrix "z(" line should be followed by "A C G T": ACGTzaA 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 ("02dz"), 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 "//)alphabetcounts)r!stripsplitlen ValueError partitionr"intzipappendfloatrupdate referencesrr)handlestrict annotationsrJr?recordline key_valuerrlengthcivaluesvindex separator accession referencemotifrrrreadbs                              r[c sFg}z|j}Wn tyYnw|durd|}||tj}d}|D]g}|D]}d}|D]} | dkrj} | dkr?q1j} tj} d dg| } || t | D].d d gd d | Dd } | t d gfdd | D| g} || qXd}n;z | }Wn tyd}Ynw|dur| |vr|D]}| d|} || qn | d|} || d}| dkrzj }Wn tyYq1wd}|D]}|D]} | | }|durq| d|} || d}qqq1|rd} || q+d} || d |d}||q%d |}|S)z7Write the representation of a motif in TRANSFAC format.Nz VV %s XX // ))ACAS)ID)rCO)NA)DE)TY)OSOC)r r )r)r,)BA)r)r)r)r PVFr,rz  z%02.dcSsg|]}dqS)z%6.20gr.0_rrr szwrite..z %sr'csg|] }j|qSr)r?rhrSrZrrrksTr*rf)r8rr rr r7r= )r"AttributeErrorrGrrrQdegenerate_consensussortedr>joinrangetuplegetrJ)rblocksr"blockrsectionslinessectionblankrrQsequencelettersrOrrUrJkeysrYtextrrlrr%s                  r%N)T) rBiorrdictlistr!r[r%rrrrs A