B ‰°bçPã@sÀdZGdd„dƒZGdd„dƒZGdd„dƒZGdd„dƒZGd d „d ƒZGd d „d ƒZGd d„dƒZGdd„dƒZGdd„dƒZ Gdd„dƒZ Gdd„dƒZ dd„Z Gdd„dƒZ dd„ZdS)a“Parser 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 ususal 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@seZdZdZdd„ZdS)Úrdz‡RD (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)zInitialize the class.ÚN)ÚnameÚ padded_basesÚ info_itemsÚ read_tagsÚsequence)Úself©r ú1lib/python3.7/site-packages/Bio/Sequencing/Ace.pyÚ__init__Cs z rd.__init__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r r r r r r=src@seZdZdZddd„ZdS)ÚqazIQA (read quality), including which part if any was used as the consensus.NcCs`d|_d|_d|_d|_|r\| ¡}t|dƒ|_t|dƒ|_t|dƒ|_t|dƒ|_dS)zInitialize the class.Néééé)Zqual_clipping_startZqual_clipping_endZalign_clipping_startZalign_clipping_endÚsplitÚint)rÚlineÚheaderr r r r Osz qa.__init__)N)r r rrr r r r r rLsrc@seZdZdZddd„ZdS)Údsz:DS lines, include file name of a read's chromatogram file.Nc sØd|_d|_d|_d|_d|_d|_d|_ˆrÔdddddddg}‡fd d „|Dƒ}tt||ƒƒ}d |krn|d =t |ƒ}x\t||d d …t ˆƒd gƒD]8\}}t |||  ¡ˆ|t ||ƒd |…  ¡ƒq˜Wd S)zInitialize the class.rZ CHROMAT_FILEZPHD_FILEZTIMEZCHEMZDYEÚTEMPLATEZ DIRECTIONcsg|]}ˆ |¡‘qSr )Úfind)Ú.0Úx)rr r ú sszds.__init__..éÿÿÿÿrN)Z chromat_fileZphd_fileZtimeZchemZdyeÚtemplateÚ directionÚdictÚzipÚsortedÚlenÚsetattrÚlowerÚstrip)rrZtagsZpossZtagposZpsZp1Zp2r )rr r `s2* z ds.__init__)N)r r rrr r r r r r]src@seZdZdZddd„ZdS)ÚafzðAF 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. NcCsDd|_d|_d|_|r@| ¡}|d|_|d|_t|dƒ|_dS)zInitialize the class.rNrrr)rZcoruÚ padded_startrr)rrrr r r r ˆs  z af.__init__)N)r r rrr r r r r r)€sr)c@seZdZdZddd„ZdS)ÚbszKBS (base segment), which read was chosen as the consensus at each position.NcCsHd|_d|_d|_|rD| ¡}t|dƒ|_t|dƒ|_|d|_dS)zInitialize the class.rNrrr)rr*Ú padded_endrr)rrrr r r r —sz bs.__init__)N)r r rrr r r r r r+”sr+c@seZdZdZddd„ZdS)ÚrtzSszparse..zAF zUnexpected end of AF blockzUnexpected end of filezBS zFailed to find end of BS blockzRD zFailed to find RD linerzQA zFailed to find QA linezDS zRT{zCOMMENT{ézC}Ú}zWR{zWA{zFailed to read WA blockzCT{zFailed to read CT blockZRD)ÚopenÚ TypeErrorÚreadÚ ValueErrorÚ startswithÚnextÚ StopIterationr;r(rr=Úextendrr)Úappendr+r>r:rrrr-r3Úendswithr9r8r7r4Úclose)ÚsourceÚhandlerÚrecordr r r Úparse!s<                                                    rPc@s eZdZdZdd„Zdd„ZdS)Ú ACEFileRecordzHolds data of an ACE file.cCsd|_d|_g|_d|_dS)zInitialize the class.N)Úncontigsr<Úcontigsr8)rr r r r ÿszACEFileRecord.__init__c s”g}g}g}x*t|jƒD]\}‰ˆjrD|js6g|_|j ˆj¡ˆjrˆ‡fdd„ˆjDƒ}x|D]}|j|j |¡qdW| |¡x¬tˆjƒD]ž\}‰ˆjræ‡fdd„ˆjDƒ}x$|D]}|j|j|j |¡q¼W| |¡ˆjr”‡fdd„ˆjDƒ} x&| D]}|j|j|j |¡qW| | ¡q”WqWxRt|jƒD]B\}‰xL|D]D} | j ˆj krX|j|jdkrˆg|j|_|j|j  | ¡qXW|s¬|rHxÜtˆjƒD]Î\}‰x`|D]X} | j ˆj j krÆ|j|j|jdkrg|j|j|_|j|j|j  | ¡qÆWx`|D]X} | j ˆj j kr(|j|j|jdkrfg|j|j|_|j|j|j  | ¡q(Wq¸WqHWdS)zRSorts wr, rt and ct tags into the appropriate contig / read instance, if possible.csg|]}|jˆjkr|‘qSr )r)rÚct_tag)Úcr r rsz&ACEFileRecord.sort..csg|]}|jˆjjkr|‘qSr )rr)rÚrt_tag)Úrr r rscsg|]}|jˆjjkr|‘qSr )rr)rÚwr_tag)rWr r rsN) Ú enumeraterSr8rIr4Úremover>r-r9rrJr) rr4r-r9ÚiZnewctsrÚjZnewrtsZnewwrsrTrVrXr )rUrWr ÚsortsT          zACEFileRecord.sortN)r r rrr r]r r r r rQüsrQcCsŠt|ƒ}tƒ}y t|ƒ}Wntk r8tdƒd‚YnX| d¡sLtdƒ‚| ¡}t|dƒ|_t|dƒ|_ t t |ƒƒ|_ |  ¡|S)z-Parse a full ACE file into a list of contigs.zPremature end of fileNZASzFile does not start with 'AS'.rr)ÚiterrQrGrHrErFrrrRr<ÚlistrPrSr])rNrOrZwordsr r r rD6s  rDN)rrrrr)r+r-r4r8r9r:r;rPrQrDr r r r Ú:s#\: