o RŀgR@s>dZddlZddlmZddlmZddlmZddlmZddlm Z ddl m Z dd l m Z dd l mZdd l mZdd l mZdd lmZddddZedZedZddZd,ddZddZddZddZddZdd Zd!d"Zd-d$d%ZGd&d'd'eZ Gd(d)d)e Z!e"d*krdd+l#m$Z$e$dSdS).zGBio.SearchIO abstract base parser for Exonerate standard output format.N)ABC)abstractmethodreduce)Optional)Type) SearchIndexer)Hit)HSP) HSPFragment) QueryResult)seq1)+-.z(#+)z[53ISCF]cCs0|jdd|j|_|jdd|j|_dS)z%Set the HSPFragment frames (PRIVATE).rN) hit_start hit_strand hit_frame query_start query_strand query_frame)fragrR/var/www/html/myenv/lib/python3.10/site-packages/Bio/SearchIO/ExonerateIO/_base.py _set_framesrcsd|d|}||dtd}|sdnd|d}fddttdD}|||fS)a Select a valid amino acid sequence given a 3-letter code input (PRIVATE). This function takes a single three-letter amino acid sequence and the phase of the sequence to return the longest intact amino acid sequence possible. Parts of the input sequence before and after the selected sequence are also returned. This is an internal private function and is meant for parsing Exonerate's three-letter amino acid output. >>> from Bio.SearchIO.ExonerateIO._base import _make_triplets >>> _make_triplets('GlyThrSerAlaPro') ('', ['Gly', 'Thr', 'Ser', 'Ala', 'Pro'], '') >>> _make_triplets('yThrSerAla', phase=1) ('y', ['Thr', 'Ser', 'Ala'], '') >>> _make_triplets('yThrSerAlaPr', phase=1) ('y', ['Thr', 'Ser', 'Ala'], 'Pr') Nrrcs$g|]}d|d|dqS)rrr).0inp_seqrr <s$z"_make_triplets..)lenrange)seqphasepre non_tripletspostintactsrr!r_make_triplets$s    r,cCs&|sgSdg}tdd|dd|S)aReturn the letter coordinate of the given list of fragments (PRIVATE). This function takes a list of three-letter amino acid sequences and returns a list of coordinates for each fragment had all the input sequences been flattened. This is an internal private function and is meant for parsing Exonerate's three-letter amino acid output. >>> from Bio.SearchIO.ExonerateIO._base import _get_fragments_coord >>> _get_fragments_coord(['Thr', 'Ser', 'Ala']) [0, 3, 6] >>> _get_fragments_coord(['Thr', 'SerAlaPro', 'GlyLeu']) [0, 3, 12] >>> _get_fragments_coord(['Thr', 'SerAlaPro', 'GlyLeu', 'Cys']) [0, 3, 12, 18] rcSs||dt|gS)Nr)r$)accrrrrWsz&_get_fragments_coord..Nrr)fragsinitrrr_get_fragments_coord@sr1cCsddt|DS)aoReturn the phases of the given list of 3-letter amino acid fragments (PRIVATE). This is an internal private function and is meant for parsing Exonerate's three-letter amino acid output. >>> from Bio.SearchIO.ExonerateIO._base import _get_fragments_phase >>> _get_fragments_phase(['Thr', 'Ser', 'Ala']) [0, 0, 0] >>> _get_fragments_phase(['ThrSe', 'rAla']) [0, 1] >>> _get_fragments_phase(['ThrSe', 'rAlaLeu', 'ProCys']) [0, 1, 0] >>> _get_fragments_phase(['ThrSe', 'rAlaLeuP', 'roCys']) [0, 1, 2] >>> _get_fragments_phase(['ThrSe', 'rAlaLeuPr', 'oCys']) [0, 1, 1] cSsg|] }d|ddqS)rrrxrrrr#msz(_get_fragments_phase..)r1)r/rrr_get_fragments_phaseZsr4cCsddd}|dj}|dj}t|}t||D]\}}|jdks(|jdks(J|jdkr/dnd}||_t|jj }t ||\} } } t|j j } t | |\} }}| rTdnd}|rZdnd}t d ||d }|t||}|t|dd|}| r}dnd}| rdnd}t d | |d }|t|}|t|dd}d |_ d |_||||_ ||||_|jdkr|||_|_n |jdkr|||_|_|jD]!\}}t ||\}}}ttd |g|ttd |g|j|<q||}}q|S) zTransform 3-letter AA codes of input fragments to one-letter codes (PRIVATE). Argument fraglist should be a list of HSPFragments objects. *r)z***z<->rrrXr) custom_mapN)rrr4ziprrr'strqueryr&r,hitr joinr$replace query_endhit_endaln_annotationitemslistfilter)fraglistr7 hsp_hstart hsp_qstart frag_phasesrr'hstepqseqq_triplets_pre q_tripletsq_triplets_posthseqh_triplets_pre h_tripletsh_triplets_post hseq1_pre hseq1_posthseq1hstarthend qseq1_pre qseq1_postqseq1qstartqendannotannotseqr(intactr*rrr_adjust_aa_seqpsH            " r^csF|jd}|ddksJg}|jdkrdnd}|jdkr dnd}|dkr+t|jnt|j}|dkr9t|jnt|j}d}|r!zt t | d}| |} | t |} |||| Wntyxd}d} t |} ||dYnw||} } |t tfdd d D|7}|t tfd d d D|7}t| |_t| |_t| |_t| |_t|| || } t |jd kr|| jj|| jjf}nt |jd kr|| jd|| jdf}d|dvr|t ||7}nd|dvr |t ||7}t||| d}|| 7}|sC|S)zLSplit one HSPFragment containing frame-shifted alignment into two (PRIVATE). similarity#rrrrNc3|] }jj|VqdSN)r:r&countr2splitrr z"_split_fragment..)r<>c3rarb)r;r&rcr2rdrrrfrgrquery_annotationhit_annotation)r@rcrrmin query_rangemax hit_rangeresearch _RE_SHIFTSgroupfindr$AttributeErrorsumrrr?r>slicer:r&r;rappend)rsimil split_fragsqsteprHqposhposabs_posshiftss_starts_stoprYrT abs_sliceseqsrrdr_split_fragmentsd              /rc Csg}t|dD]\}}|d}|durdn||}|d}|dur&dn||} t|||| d} |d| _|d| _|d |d| _|d |d| _z|d i} | D] \} } | || j| <qYWn t yoYnw|d | _ |d | _ | jd durd| jd vr| t | qt| jdks| j dksd|vrtt|drt| || qt|djdkrt|}t|}dD]}||vrt||||q|S)zHReturn a list of HSP objects from the given parsed HSP values (PRIVATE). query_rangesr;Nrr:)r;r:rr hit_rangesr@rrr_r` vulgar_comprj)scorehit_split_codonsquery_split_codonsmodelr cigar_comp molecule_type) enumerategetr rr>rr?rAr@ IndexErrorrrextendrr$rqrr _RE_TRANSrryr^r setattr)hidqidhspdr/idxqcoordshseqlistrMqseqlistrIr aln_annotkeyvaluehspattrrrr _create_hspsL           rcCsJz|dd\}}}W||fSty$|dd\}}d}Y||fSw)zAParse the 'Query:' line of exonerate alignment outputs (PRIVATE). rjrr)re ValueError)linemarkiddescrrr_parse_hit_or_query_line3s rTcCsZ|rd|fSd}|dr|drdnd}|sd|fS|r)d|dt| fSd|fS)a8Determine the strand from the description (PRIVATE). Exonerate appends ``:[revcomp]`` (versions <= 2.2) or ``[revcomp]`` (versions > 2.2) to the query and/or hit description string. This function outputs '-' if the description has such modifications or '+' if not. If the query and/or hit is a protein sequence, a '.' is output instead. Aside from the strand, the input description value is also returned. It is returned unmodified if ``modify_desc`` is ``False``. Otherwise, the appended ``:[revcomp]`` or ``[revcomp]`` is removed. rrz [revcomp]z :[revcomp]rrN)endswithr$)r is_protein modify_descsuffixrrr_get_strand_from_desc>s  rc@sVeZdZUdZdZeeed<ddZddZ dd Z e d d Z d d Z ddZdS)_BaseExonerateParserz2Abstract base class iterator for exonerate format.N _ALN_MARKcCs||_d|_dS)NF)handlehas_c4_alignment)selfrrrr__init__`s z_BaseExonerateParser.__init__ccs |j|_|jdr|jsd|_|jds&|jds&|jdr'n |jr0|jdr2dSq|D]}d|_|j|_|D]}|j|_qB|Vq7dS)NT C4 Alignment:zvulgar:zcigar: -- completed exonerate)rreadliner startswithr_parse_qresultprogram description)rqresultr;rrr__iter__ds,      z_BaseExonerateParser.__iter__cCs$ |jr ||jr dS|j|_q)z@Read the file handle until the given bool function returns True.TN)rrr)r bool_funcrrr read_until|s  z_BaseExonerateParser.read_untilcCstrbNotImplementedError)rheaderrrrparse_alignment_blocksz*_BaseExonerateParser.parse_alignment_blockc Csg}|jr||j|j|_|jsiii}}}|D]o}|dr6t|\|d<|d<q$|drFt|\|d<|d<q$|drV|ddd|d<q$|d rf|dd d |d <q$|d r}|dd d dd \|d<|d<q$|dr|dd d dd \|d<|d<q$t|dd|dvdd\}}||d<||d<t|dd|dvdd\}} ||d<| |d<|||dS)NQuery:rrzTarget:zModel:rrrz Raw score:rjrz Query range:rr>z Target range:rr?protein2T)rrrr2proteinrrr;r) rstripryrrrrrer) r aln_headerrr;rrqresult_strand qresult_descrhit_descrrr_parse_alignment_headersF        $ "     z,_BaseExonerateParser._parse_alignment_headerc#s d}d}d}d}d}d\}}d}d\} } d\} } d\} }gg}}jr(d_ fd d | dur<| }| } | } jrqjjsKJjiiid }jr_d d }|} | d d} | dd} njrzjdr|}d\} } | | kr|}n|}| | ks||kr|}n|}|durt| | |d}||||krt |}|d D] \}}t |||q||g}||ks||krt | d}|D]}| |q|d  D] \}}t |||q|V||krdSg}jsj_q))Nrrrrjr)NNrTcs |jSrb)rrrrrrr.s z5_BaseExonerateParser._parse_qresult..rcSs|dS)Nr)rrrrrrr.srrr;rr)r)rrrrrrrrryr rArr absorbrr)r state_EOFstate_QRES_NEWstate_QRES_SAME state_HIT_NEWstate_HIT_SAME qres_state hit_state file_statecur_qidcur_hidprev_qidprev_hidcurprevhit_listhsp_listrrr;rrrrrrrsx         z#_BaseExonerateParser._parse_qresult)__name__ __module__ __qualname____doc__rrr9__annotations__rrrrrrrrrrrr[s   7rc@sFeZdZUdZdZeeeed<dZ ee ed<ddZ ddZ dS) _BaseExonerateIndexerz'Indexer class for Exonerate plain text.N_parser _query_markcCstd)NzShould be defined by subclassr)rposrrrget_qresult_idsz$_BaseExonerateIndexer.get_qresult_idccs|j}|dd} |}|}||jrA|dur&||}|}n'||}||kr@||||fV|}|}||n |sM||||fVdSq )zCIterate over the file handle; yields key, start offset, and length.rN)_handleseektellrrrr)rr qresult_key start_offsetrqresult_offsetcurr_keyrrrrs,     z_BaseExonerateIndexer.__iter__) rrrrrrrrrrbytesrrrrrrrs  r__main__) run_doctest)r)T)%rrqabcrr functoolsrtypingrrBio.SearchIO._indexrBio.SearchIO._modelr r r r Bio.SeqUtilsr _STRAND_MAPcompilersrrr,r1r4r^rrrrrrr Bio._utilsrrrrrs@               AB@ 8%