o RŀgP@sdZGdddZGdddZGdddZGdddZGd d d ZGd d d ZGd ddZGdddZGdddZ GdddZ GdddZ ddZ GdddZ ddZdS)aParser for ACE files output by PHRAP. Written by Frank Kauff (fkauff@duke.edu) and Cymon J. Cox (cymon@duke.edu) Usage: There are two ways of reading an ace file: 1. The function 'read' reads the whole file at once; 2. The function 'parse' reads the file contig after contig. First option, parse whole ace file at once:: from Bio.Sequencing import Ace acefilerecord = Ace.read(open('my_ace_file.ace')) This gives you: - acefilerecord.ncontigs (the number of contigs in the ace file) - acefilerecord.nreads (the number of reads in the ace file) - acefilerecord.contigs[] (one instance of the Contig class for each contig) The Contig class holds the info of the CO tag, CT and WA tags, and all the reads used for this contig in a list of instances of the Read class, e.g.:: contig3 = acefilerecord.contigs[2] read4 = contig3.reads[3] RD_of_read4 = read4.rd DS_of_read4 = read4.ds CT, WA, RT tags from the end of the file can appear anywhere are automatically sorted into the right place. see _RecordConsumer for details. The second option is to iterate over the contigs of an ace file one by one in the usual way:: from Bio.Sequencing import Ace contigs = Ace.parse(open('my_ace_file.ace')) for contig in contigs: print(contig.name) ... Please note that for memory efficiency, when using the iterator approach, only one contig is kept in memory at once. However, there can be a footer to the ACE file containing WA, CT, RT or WR tags which contain additional meta-data on the contigs. Because the parser doesn't see this data until the final record, it cannot be added to the appropriate records. Instead these tags will be returned with the last contig record. Thus an ace file does not entirerly suit the concept of iterating. If WA, CT, RT, WR tags are needed, the 'read' function rather than the 'parse' function might be more appropriate. c@seZdZdZddZdS)rdzRD (reads), store a read with its name, sequence etc. The location and strand each read is mapped to is held in the AF lines. cCs"d|_d|_d|_d|_d|_dS)Initialize the class.N)name padded_bases info_items read_tagssequenceselfr F/var/www/html/myenv/lib/python3.10/site-packages/Bio/Sequencing/Ace.py__init__Cs  z rd.__init__N__name__ __module__ __qualname____doc__r r r r r r=s rc@eZdZdZdddZdS)qazIQA (read quality), including which part if any was used as the consensus.NcCsdd|_d|_d|_d|_|r0|}t|d|_t|d|_t|d|_t|d|_dSdSrN)qual_clipping_startqual_clipping_endalign_clipping_startalign_clipping_endsplitintr lineheaderr r r r Osz qa.__init__Nrr r r r rLrc@r)dsz:DS lines, include file name of a read's chromatogram file.Nc sd|_d|_d|_d|_d|_d|_d|_rcgd}fdd|D}tt||}d|vr2|d=t |}t||ddt dgD]\}}t ||| |t ||d| qFdSdS)rr) CHROMAT_FILEPHD_FILETIMECHEMDYETEMPLATE DIRECTIONcsg|]}|qSr )find.0xr!r r sszds.__init__..rN) chromat_filephd_filetimechemdyetemplate directiondictzipsortedlensetattrlowerstrip)r r!tagsposstagpospsp1p2r r1r r `s, ( z ds.__init__r#rr r r r r%]r$r%c@r)afzAF lines, define the location of the read within the contig. Note attribute coru is short for complemented (C) or uncomplemented (U), since the strand information is stored in an ACE file using either the C or U character. NcCsHd|_d|_d|_|r"|}|d|_|d|_t|d|_dSdSrrNrrr)rcoru padded_startrrr r r r r s  z af.__init__r#rr r r r rHsrHc@r)bszKBS (base segment), which read was chosen as the consensus at each position.NcCsLd|_d|_d|_|r$|}t|d|_t|d|_|d|_dSdSrI)rrK padded_endrrr r r r r sz bs.__init__r#rr r r r rLr$rLc@r)rtzr r r r r s*     z ct.__init__r#rr r r r rUr$rUc@r)wazGWA (whole assembly tag), holds the assembly program name, version, etc.NcCsJd|_d|_d|_g|_|r#|}|d|_|d|_|d|_dSdS)rrrOrrN)rQrRrSrYrr r r r r s  z wa.__init__r#rr r r r rZr$rZc@r)wrz WR lines.NcCsTd|_d|_d|_g|_|r(|}|d|_|d|_|d|_|d|_dSdS)rrrOrrrN)ralignedrRrSrr r r r r s   z wr.__init__r#rr r r r r[r$r[c@r)Readsz8Holds information about a read supporting an ACE contig.NcCsvd|_d|_d|_d|_d|_|r9t|_|}|d|j_t|d|j_t|d|j_ t|d|j_ dSdSr) rrr%rNr[rrrrrrr r r r r s zReads.__init__r#rr r r r r]r$r]c@r)Contigz4Holds information about a contig from an ACE record.NcCsd|_d|_d|_d|_d|_d|_g|_g|_g|_g|_ d|_ d|_ |rK| }|d|_t |d|_t |d|_t |d|_|d|_dSdS)rrNrrrrrP)rnbasesnreads nsegmentsuorcrqualityrHrLreadsrUrZrrr r r r r s( zContig.__init__r#rr r r r r^r$r^ccszt|}Wnty|}|ddkrtddYnwzd} z |dr,nt|}q&WntyGYW||urE|dSdSwt|}|D]}| }|sXn|j |7_ qN|D]}| rjnqb|dsttd|D]}| s~n|j d d | Dqv|D]}| rnq |d sn|jt|zt|}Wn tytd dwq | rnzt|}Wn tytd dwq |dsn|jt|zt|}Wn tytddwq z |drnt|}qWn tytddw|jt||D]}| }|s*n |jdjj |7_ q|D] }| rBnq9|dsNtdt||jd_|D] }| ranqXn|drut||jd_d} z | r~nt|}qxWn tyYn]w|dr|jdjdurg|jd_|D]X}| }|dr|dd r|jdjdj|dd|D]}| }|drn|jdjdj|qϐq|dkrn |jdjt|qd}n|dr8|jdjdurg|jd_|D]}| }|dkr(n |jdjt|qd}n|dr|jdurGg|_zt|}Wn tyZtddw|jt||D]}| }|dkrrn |jdj|qed}nk|dr|jdurg|_zt|}Wn tytddw|jt||D]9}| }|dkr|D]}| }|drn |jdj|qq|dkrn |jdj|qd}nnqv|d snq|Vq$||ur|ww)!akIterate of ACE file contig by contig. Argument source is a file-like object or a path to a file. This function returns an iterator that allows you to iterate over the ACE file record by record:: records = parse(source) for record in records: # do something with the record where each record is a Contig object. rOrz&Ace files must be opened in text mode.NTCOBQzFailed to find BQ linecss|]}t|VqdSr#)rr.r r r Sszparse..zAF zUnexpected end of AF blockzUnexpected end of filezBS zFailed to find end of BS blockzRD zFailed to find RD liner3zQA zFailed to find QA linezDS zRT{zCOMMENT{zC}}zWR{zWA{zFailed to read WA blockzCT{zFailed to read CT blockRD)open TypeErrorread ValueError startswithnext StopIterationcloser^rArrcextendrrHappendrLrdr]rrr%rNrTendswithr[rZrYrU)sourcehandler!recordr r r parse!s     8                                           Pz @ ryc@s eZdZdZddZddZdS) ACEFileRecordzHolds data of an ACE file.cCsd|_d|_g|_d|_dS)rN)ncontigsr`contigsrZr r r r r s zACEFileRecord.__init__c sNg}g}g}t|jD]\}jr|jsg|_|jjjr?fddjD}|D] }|j|j|q.||tjD]J\}jrkfddjD}|D]}|j|j|j|qW||jrfddjD} | D]}|j|j|j|qz|| qDq t|jD]\}|D]} | j j kr|j|jdurg|j|_|j|j | q|s|r$tjD]^\}|D])} | j j j kr|j|j|jdurg|j|j|_|j|j|j | q|D]+} | j j j kr"|j|j|jdurg|j|j|_|j|j|j | qqqdS)zRSorts wr, rt and ct tags into the appropriate contig / read instance, if possible.csg|] }|jjkr|qSr )r)r/ct_tag)cr r r2sz&ACEFileRecord.sort..cg|] }|jjjkr|qSr rr)r/rt_tagrr r r2crr r)r/wr_tagrr r r2rN) enumerater|rZrsrUremoverdrNr[rrtr) r rUrNr[inewctsr0jnewrtsnewwrsr}rrr )r~rr sortsd       zACEFileRecord.sortN)rrrrr rr r r r rzs rzcCst|}t}zt|}Wn tytddw|ds#td|}t|d|_t|d|_ t t ||_ | |S)z-Parse a full ACE file into a list of contigs.zPremature end of fileNASzFile does not start with 'AS'.rr)iterrzrprqrnrorrr{r`listryr|r)rwrxr!wordsr r r rm5s    rmN)rrrr%rHrLrNrUrZr[r]r^ryrzrmr r r r s 6#[ :