ó ÊOIc @sFdZddlmZddlmZdddddd d d d d ddg Zdd#d„ƒYZd„Zd„Zddlm Z ddl Tdd$d„ƒYZ de fd„ƒYZ dd%d„ƒYZdefd„ƒYZedkrBdGHed ƒZeeƒZx#eD]ZejGeejƒGHqWejƒd!GHnd"S(&sX Parser for PHD files output by PHRED and used by PHRAP and CONSED. This module can be used used directly which will return Record objects which should contain all the original data in the file. Alternatively, using Bio.SeqIO with the "phd" format will call this module internally. This will give SeqRecord objects for each contig sequence. iÿÿÿÿ(tSeq(t generic_dnat CHROMAT_FILEtABI_THUMBPRINTt PHRED_VERSIONt CALL_METHODtQUALITY_LEVELStTIMEtTRACE_ARRAY_MIN_INDEXtTRACE_ARRAY_MAX_INDEXtTRIMtTRACE_PEAK_AREA_RATIOtCHEMtDYEtRecordcBseZdZd„ZRS(s!Hold information from a PHD file.cCsUd|_i|_x!tD]}d|j|jƒ((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pytparseps  (tFile(t*tIteratorcBs,eZdZdd„Zd„Zd„ZRS(sIterates over a file of multiple PHD records (DEPRECATED). Methods: next Return the next record from the stream, or None. cCs;ddl}|jdtƒtj|ƒ|_||_dS(sCreate a new iterator. Create a new iterator. handle is a file-like object. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. iÿÿÿÿNs•Bio.Sequencing.Phd.Iterator is deprecated. Please use Bio.Sequencing.Phd.parse(handle) instead of Bio.Sequencing.Phd.Iterator(handle, RecordParser())(twarningstwarntDeprecationWarningRKt UndoHandlet_uhandlet_parser(RR<tparserRN((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyR‘s cCs¢g}xT|jjƒ}|s"Pn|rL|d dkrL|jj|ƒPn|j|ƒq W|sgdSdj|ƒ}|jdk rž|jjtj |ƒƒS|S(NiRR( RRtreadlinetsavelineR:RR;RSRJRKt StringHandle(RtlinesR=tdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pytnextscCst|jdƒS(s+Iterate over the PHY file record by record.N(titerRZR(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyt__iter__±sN(RRRRRRZR\(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRMŠs t RecordParsercBs eZdZd„Zd„ZRS(s7Parses PHD file data into a Record object (DEPRECATED).cCs8ddl}|jdtƒtƒ|_tƒ|_dS(Niÿÿÿÿs”Bio.Sequencing.Phd.RecordParser is deprecated. Please use Bio.Sequencing.Phd.read(handle) instead of Bio.Sequencing.Phd.RecordParser().parse(handle)(RNRORPt_Scannert_scannert_RecordConsumert _consumer(RRN((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyR·s  cCsJt|tjƒr|}ntj|ƒ}|jj||jƒ|jjS(N(t isinstanceRKRQR_tfeedRaRY(RR<tuhandle((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRJ½s  (RRRRRJ(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyR]µs R^cBs;eZdZd„Zd„Zd„Zd„Zd„ZRS(s_Scans a PHD-formatted file (DEPRECATED). Methods: feed - Feed one PHD record. cCsAt|tjƒstdƒ‚|jƒr=|j||ƒndS(s÷Reads in PDH data from the handle for scanning. Feed in PHD data for scanning. handle is a file-like object containing PHD data. consumer is a Consumer object that will receive events as the PHD data is scanned. shandle must be an UndoHandleN(RbRKRQtAssertionErrortpeeklinet _scan_record(RR<tconsumer((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRcÌs  cCs>|j||ƒ|j||ƒ|j||ƒ|jƒdS(N(t_scan_begin_sequencet_scan_commentst _scan_dnat end_sequence(RRdRh((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRgØscCst||jddƒdS(NtstartR(t read_and_calltbegin_sequence(RRdRh((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRiÞscCs·t||jddƒt||jddƒt||jddƒxBx;tD]2}t|t||jƒƒd|dƒrLPqLqLWPqEWt||jddƒt||jddƒdS(NtblankiRmRR!R (tread_and_call_whiletnoeventRnRtattempt_read_and_calltgetattrR(RRdRhR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRjás (cCsRxK|jƒ}t|ƒs|dkr-qn|dkr=Pn|j|ƒqWdS(Ns BEGIN_DNA sEND_DNA (RUt is_blank_linetread_dna(RRdRhR=((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRkñs  (RRRRcRgRiRjRk(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyR^Æs    R`cBsžeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z d „Zd „Zd„Zd„Zd„ZRS(sDConsumer that converts a PHD record to a Record object (DEPRECATED).cCs d|_dS(N(RRY(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRýscCs&tƒ|_|djƒ|j_dS(Ni(RRYR4R(RR=((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRos cCsœtjdjg|jjD]}|d^qƒtƒ|j_|jjddk r˜|jjdd}|jjdd}|jj||!|j_ndS(NRiR/i( RR;RYRRRRRR(RRGRARB((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyRls >cCs!|dd!jƒ|jjdRtlenRtclose(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Phd.pyts,   M  +59