o Rŀg6@sdZddlmZddlmZddlmZddlmZddlmZddlm Z dd lm Z d Z Gd d d e Z Gd dde Z Gddde ZGddde ZGddde ZGdddZGdddeZedkrtddlmZedSdS)z9Bio.SearchIO parser for HMMER domain table output format.)chain)Hit)HSP) HSPFragment) QueryResult)Hmmer3TabIndexer)Hmmer3TabParser)Hmmer3DomtabHmmhitParserHmmer3DomtabHmmqueryParserHmmer3DomtabHmmhitIndexerHmmer3DomtabHmmqueryIndexerHmmer3DomtabHmmhitWriterHmmer3DomtabHmmqueryWriterc@s eZdZdZddZddZdS)Hmmer3DomtabParserzBase hmmer3-domtab iterator.cCs8|jsJdd|jdD}t|dkr$d|dd|d<nt|dkr7|dt|dks7Ji}|d|d <|d |d <t|d |d <i}|d|d <|d|d <t|d|d <t|d|d<t|d|d<t|d|d<|d|d<i}t|d|d<t|d|d<t|d|d<t|d|d<t|d|d<t|dd|d <t|d!|d"<t|d#|d$<i}d|d%<|d&<t|d'd|d(<t|d)|d*<t|d+d|d,<t|d-|d.<d/|d0<|js|d.|d*|d*<|d.<|d,|d(|d(<|d,<||||d1S)2z3Return a dictionary of parsed row values (PRIVATE).cSsg|]}|r|qSr).0xrrV/var/www/html/myenv/lib/python3.10/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py "sz1Hmmer3DomtabParser._parse_row.. Nid accessionseq_lenrrevaluebitscorebias description domain_index evalue_cond  env_startenv_endacc_avg hit_strand query_strand hit_starthit_end query_start query_endprotein molecule_type)qresulthithspfrag) linestripsplitlenjoinappendintfloat hmm_as_hit)selfcolsrArBrCrDrrr _parse_rowsR         zHmmer3DomtabParser._parse_rowccsd}d}d}d}d}d}d}d}d} d} d\} } gg} }d}d} | dur-| } |} |} |jrG|jd sG|} | d d }| d d }n|}d\}}| |krT|}n|}| |ks^||kra|}n|}| durt| | }| d D] \}}t|||qrt|g}| dD] \}}t|||q||||krt|}| d D] \}}t|||q| |g}||ks||krt | | }| d D] \}}t|||q|V||krdSg} |j |_q#)z%Return QueryResult objects (PRIVATE).rrrr rN)NNT#rArrBrDrC) rE startswithrPritemssetattrrrJrrhandlereadline)rN state_EOFstate_QRES_NEWstate_QRES_SAME state_HIT_NEWstate_HIT_SAME qres_state hit_state file_stateprev_qidprev_hidcurprevhit_listhsp_listcur_qidcur_hidrDattrvaluerCrBrArrr_parse_qresultVsp        z!Hmmer3DomtabParser._parse_qresultN)__name__ __module__ __qualname____doc__rPrirrrrrs 7rc@eZdZdZdZdS)r zHMMER domain table parser using hit coordinates. Parser for the HMMER domain table format that assumes HMM profile coordinates are hit coordinates. TNrjrkrlrmrMrrrrr r c@rn)r zHMMER domain table parser using query coordinates. Parser for the HMMER domain table format that assumes HMM profile coordinates are query coordinates. FNrorrrrr rpr c@eZdZdZeZdZdS)r zHMMER domain table indexer using hit coordinates. Indexer class for HMMER domain table output that assumes HMM profile coordinates are hit coordinates. rN)rjrkrlrmr _parser _query_id_idxrrrrr r c@rq)r zHMMER domain table indexer using query coordinates. Indexer class for HMMER domain table output that assumes HMM profile coordinates are query coordinates. rN)rjrkrlrmr rrrsrrrrr rtr c@s6eZdZdZdZddZddZd dd Zd d ZdS) rzHMMER domain table writer using hit coordinates. Writer for hmmer3-domtab output format which writes hit coordinates as HMM profile coordinates. TcCs ||_dS)zInitialize the class.N)rU)rNrUrrr__init__s z!Hmmer3DomtabHmmhitWriter.__init__c Cs|j}d\}}}}zt|}Wnty||Ynsz6Hmmer3DomtabHmmhitWriter.write_file..css|]}t|jVqdSrv)rH fragmentsrwrrrrxs) rUnext StopIterationwrite _build_headerr _build_rowrHsum) rNqresultsrUqresult_counter hit_counter hsp_counter frag_counter first_qresultrArrr write_files"     z#Hmmer3DomtabHmmhitWriter.write_fileNcCs&|r0d}tdt|dj}ztdt|j}tdt|dj}Wnty/d\}}Ynwd\}}}}d||dd||d d d d d df}|d|dd|dd|d|dddddddddddddddddddf7}|d |dd!|d"d#|d$|d"d#d%d&d#d'd'd%d%d&d#d#d#d#d#d#d#d(d)f7}|S)*zBReturn the header string of a domain HMMER table output (PRIVATE).r1r rr)r1r1rrz#%*s %22s %40s %11s %11s %11s rr7rz--- full sequence ---z(-------------- this domain -------------z hmm coordz ali coordz env coordz`#%-*s %-*s %5s %-*s %-*s %5s %9s %6s %5s %3s %3s %9s %9s %6s %5s %5s %5s %5s %5s %5s %5s %4s %s z target namertlenz query nameqlenzE-valuescorer&rQofzc-Evaluezi-Evaluefromtoacczdescription of targetz\#%*s %*s %5s %*s %*s %5s %9s %6s %5s %3s %3s %9s %9s %6s %5s %5s %5s %5s %5s %5s %5s %4s %s z-------------------z ----------z-----z--------------------z ---------z------z---z----z---------------------)maxrHrrAttributeError)rNrqnamewtnamewqaccwtaccwheaderrrrr}sH         z&Hmmer3DomtabHmmhitWriter._build_headercCsfd}tdt|j}tdt|dj}ztdt|j}tdt|dj}|j}Wnty:d\}}d}Ynw|D]s}z|j} Wn tyOd} Ynw|jD]\} |jri| j} | jd} | j } | j d}n| j } | j d} | j} | jd}|d||j|| |j ||j|||j |j |j |j| jt|j| j| j | j | j| | || | jd| j| j|jf7}qSq=|S) zGReturn a string or one row or more of the QueryResult object (PRIVATE).rr1rrr-rzq%-*s %-*s %5d %-*s %-*s %5d %9.2g %6.1f %5.1f %3d %3d %9.2g %9.2g %6.1f %5.1f %5d %5d %5ld %5ld %5d %5d %4.2f %s )rrHrrrhspsrMr:r8r>r<rr"r$r&r)r+r0r2r4r')rNrArowsrrrr qresult_accrBhit_accrChmm_tohmm_fromali_toali_fromrrrr~#sz         /z#Hmmer3DomtabHmmhitWriter._build_rowrv) rjrkrlrmrMrurr}r~rrrrrs  *rc@rn)rzHMMER domain table writer using query coordinates. Writer for hmmer3-domtab output format which writes query coordinates as HMM profile coordinates. FNrorrrrrlrpr__main__) run_doctestN)rm itertoolsrBio.SearchIO._modelrrrr hmmer3_tabrr __all__rr r r r rrrj Bio._utilsrrrrrs,