o Rŀg@@stdZddlZddlZddlZddlmZddlmZddlm Z ddl m Z Gdddej Z Gd d d ejZdS) a Bio.Align support for tabular output from BLAST or FASTA. This module contains a parser for tabular output from BLAST run with the '-outfmt 7' argument, as well as tabular output from William Pearson's FASTA alignment tools using the '-m 8CB' or '-m 8CC' arguments. N) Alignment) interfaces)Seq) SeqRecordc@s0eZdZdZeZeZeZeZ dS)Statez=Enumerate alignment states needed when parsing a BTOP string.N) __name__ __module__ __qualname____doc__enumautoMATCH QUERY_GAP TARGET_GAPNONErrE/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/tabular.pyrs  rc@s<eZdZdZdZddZddZddZd d Zd d Z d S)AlignmentIteratora<Alignment iterator for tabular output from BLAST or FASTA. For reading (pairwise) alignments from tabular output generated by BLAST run with the '-outfmt 7' argument, as well as tabular output generated by William Pearson's FASTA alignment programs with the '-m 8CB' or '-m 8CC' output formats. TabularcCsPzt|}Wn tytddw|dstd|}|||dS)Nz Empty file.# zMissing header.)next StopIteration ValueError startswithrstrip _parse_header)selfstreamlinerrr _read_header-s    zAlignmentIterator._read_headerc Csi}d}z|dddd\}}||vrtdWn1tyK|dd|d<t|}|ds4J|dddd\|d<|d<d |_Yn w|||d<|d<d |_|D]}|}|dsgJz |ddd \}}Wntyd } || sJt|dt |  } Ynew|d kr|ddkr| dd\} } | \} } t| |_ | dvsJn|} d|_ z | dd\|_ |_ WqZty| |_ d|_ YqZw|dkr||d<qZ|dkr|d|_qZ|dkr||d<qZ||_dS)N) BLASTNBLASTPBLASTXTBLASTNTBLASTX DELTABLASTPSIBLASTRPSBLAST RPSTBLASTNzNot a BLAST programz Command linerProgramVersionz# FASTA processed z# BLAST processed z: z hits foundQueryFASTAz - )ntaaDatabaseFieldsz, RID)splitrrrr _final_prefixstripendswithintlenrsplit _query_size _query_id_query_description_fieldsmetadata)rrrr?blast_programsprogramversionprefixvaluesuffixhits query_line query_sizeunitrrrr7sb  $           zAlignmentIterator._parse_headerc Cs|D]*}|}|dr,||jr%|dr%|`|`|`|`|`dS|||qd}d}d}d}d}d}d} d} d} d} d} d}d}d}d}|j}| d}t |t |jks^Ji}i}i}t ||jD]\}}|dkr|}|jdur||jksJqj|dkr|} qj|dkrt |||<qj|dkrt |}qj|dkrt |||<qj|d krt |||<qj|d krt |} qj|d krt |} qj|d krt |} qj|d krt |} qj|dkrt ||d<qj|dkrt ||d<qj|dkr||}qj|dkr||}qj|dkr ||d<qj|dkr||d<qj|dkr'||d<|dur&|}qj|dkr@|dur6t |}qj|t |ks?Jqj|dkrJ||d<qj|dkrT||d<qj|dkr^||d<qj|dkrh||d<qj|dkrr||d <qj|d!kr|||d"<qj|d#kr||d$<qj|d%kr||d&<qj|d'kr||d(<qj|d)kr||d*<qj|d+kr||d,<qj|d-kr||d.<qj|d/kr||d0<qj|d1krt ||d2<qj|d3kr||d<| dur|} qj|d4krt |}qj|d5kr|}qj|d6kr|}qj|d7krt |}qj|d8krt |}|||<qj|d9krt |||<qj|d:kr)t |||<qj|d;kr5t |||<qj|dkrU||d?<qj|d@kr_||d?<qjtdA||jdB}|durx|durx||d<| dur| dur| | kr| dC8} n| dC8} | dur| dur| | kr| dC8} n| dC8} |dus|dDvr| dur| |dE<| dur| |dF<n'|dur| | kr|dCddf| 7<n| |dCddf|dCddf<|dus|dGvr | dur| |dE<| dur| |dF<n|dur|dHddf| 7<|dur.|dur'd}n>td|dI}n7|dJdK}|dLkrMt || | ksDJt| |i|dI}n|dMkr_| |dE<| |dF<t|}ntdN|t||dO}|jduru|j|_|r{||_|jdBdGvr||dP<|durd}nB|dJdK}t|}n7|dur| durd}n*td| dI}n#|dJdK}| dur| durt || | ksJt| |i| dI}t|| dO}|r||_||g}t||}||_|dur||_|S)QNrz queries zquery idz subject idz % identityzalignment length mismatchesz gap openszq. startzq. endzs. startzs. endevaluez bit scoreBTOPaln_codezquery gigiz query acc.zacc.z query acc.verzacc.verz query lengthz subject idsidsz subject giz subject gisgisz subject acc.z subject accs.zaccs.zsubject tax idsztax idszsubject sci namesz sci nameszsubject com namesz com nameszsubject blast namesz blast nameszsubject super kingdomszsuper kingdomsz subject titletitlezsubject titlestitleszsubject strandstrandz% subject coveragez % coveragezsubject acc.verzsubject lengthz query seqz subject seqscore identical positivesgapsz % positivesz% hsp coveragezquery/sbjct framesz query frameframez sbjct framezUnexpected field '%s'r+r*)r"r$startend)r#r$r)length-r#r$zUnknown program %s)idr\)rrr5r7r>r<r=r;rr4r9zipfloatr8 parse_btop parse_cigarrr?rreplace Exceptionr description annotationsrrU) rrralignment_lengthrVbtopcigarrUquery_id target_id query_start query_end target_start target_endquery_sequencetarget_sequence target_length coordinatesrHcolumnsrgquery_annotationstarget_annotationscolumnfieldrA query_seqquery target_seqtargetrecords alignmentrrr_read_next_alignmentss                                                                                                     z&AlignmentIterator._read_next_alignmentc CsTg}g}|d|dtj}td|}|D]}|dr?|tjkr6||d||dtj}|dd7<q|drc|tjkrZ||d||dtj}|dd7<qzt |}Wn t ytd}Ynw|tj kr|d|7<|d|7<q||d|||d|tj }qt ||g}|S)zParse a BTOP string and return alignment coordinates. A BTOP (Blast trace-back operations) string is used by BLAST to describe a sequence alignment. rz([A-Z-*]{2}|\d+)r]r*)appendrrrefindallrrr7rr8rr nparray) rritarget_coordinatesquery_coordinatesstatetokenstokenr\rtrrrrbOs@          zAlignmentIterator.parse_btopc Csg}g}d}d}||||tj}td|}t|ddd|dddD]0\}} t|}| dkr?||7}||7}n| dkrH||7}n| dkrP||7}||||q*t||g} | S) aParse a CIGAR string and return alignment coordinates. A CIGAR string, as defined by the SAM Sequence Alignment/Map format, describes a sequence alignment as a series of lengths and operation (alignment/insertion/deletion) codes. rz (M|D|I|\d+)Nr)r*MID) rrrrrr`r8rr) rrjrrtarget_coordinatequery_coordinaterrr\ operationrtrrrrc{s*   &    zAlignmentIterator.parse_cigarN) rrr r fmtrrrrbrcrrrrr"s <] ,r)r r rnumpyr Bio.AlignrrBio.Seqr Bio.SeqRecordrEnumrrrrrrs