ó ®ÒÈIc@sºdZddlmZddlmZdejfd„ƒYZdejfd„ƒYZdejfd „ƒYZd ejfd „ƒYZ d ejfd „ƒYZ dejfd„ƒYZ dejfd„ƒYZ dejfd„ƒYZ dejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZdejfd„ƒYZd ejfd!„ƒYZd"ejfd#„ƒYZd$S(%s†Code to interact with and run various EMBOSS programs. These classes follow the AbstractCommandline interfaces for running programs. iÿÿÿÿ(t Application(t_OptiontPrimer3CommandlinecBseZdZdd„ZRS(s>Commandline object for the Primer3 interface from EMBOSS. teprimer3c5CsÇtjj|ƒ||_tdgdgdddƒtdgddgdddƒtd gdgdd ƒtd gdgdd ƒtd gdgdd ƒtd gdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtdgdgdd ƒtd gdgdd ƒtd!gdgdd ƒtd"gdgdd ƒtd#gdgdd ƒtd$gdgdd ƒtd%gdgdd ƒtd&gdgdd ƒtd'gdgdd ƒtd(gdgdd ƒtd)gdgdd ƒtd*gdgdd ƒtd+gdgdd ƒtd,gdgdd ƒtd-gdgdd ƒtd.gdgdd ƒtd/gdgdd ƒtd0gdgdd ƒtd1gdgdd ƒtd2gdgdd ƒtd3gdgdd ƒtd4gdgdd ƒtd5gdgdd ƒtd6gdgdd ƒtd7gdgdd ƒtd8gdgdd ƒg1|_dS(9Ns -sequencetinputisSequence to choose primers froms-outfiletoutputtfilesOutput file names-taskis -numreturns-includedregions-targets-excludedregions -forwardinputs -reverseinputs-gcclamps-osizes-minsizes-maxsizes-otms-mintms-maxtms -maxdifftms -ogcpercents-mingcs-maxgcs -saltconcs-dnaconcs -maxployxs -productosizes-productsizeranges -productotms -productmintms -productmaxtms-oligoexcluderegions -oligoinputs -oligosizes -oligominsizes -oligomaxsizes-oligotms -oligomintms -oligomaxtms-oligoogcpercents -oligomingcs -oligomaxgcs-oligosaltconcs -oligodnaconcs -oligoselfanys -oligoselfends-oligomaxpolyxs-mispriminglibraryfiles-maxmisprimings-oligomishyblibraryfiles-oligomaxmishybs -explainflag(RtAbstractCommandlinet__init__t program_nameRtNonet parameters(tselftcmd((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR sj (t__name__t __module__t__doc__R(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR stPrimerSearchCommandlinecBseZdZdd„ZRS(sACommandline object for the primersearch program from EMBOSS. t primersearchc Cs˜tjj|ƒ||_tdgdgdddƒtdgddgdddƒtdgd dgddd ƒtd gdgddd ƒg|_dS( Ns -sequencesRis)Sequence to look for the primer pairs in.s-primersRs/File containing the primer pairs to search for.s-outRsName of the output file.s-mismatchpercentsAllowed percentage mismatch.(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRJs (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRGstEProtDistCommandlinecBseZdZdd„ZRS(szCommandline object for the eprotdist program from EMBOSS. This is an EMBOSS wrapper around protdist from PHYLIP. t eprotdistcCs tjj|ƒ||_tdgdgdddƒtdgdgdddƒtdgdgddd ƒtd gdgdd d ƒtd gdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd d ƒg|_dS(!Ns-msfRisFile containing sequencess-outfileRsOutput file names-methodsChoose the method to uses-categisChoose the categorie to uses-gencodesWhich genetic codes-probsProb change category (1.0=easy)s -tranratesTransition/transversion ratios-freqasFrequency for As-freqcsFrequency for Cs-freqgsFrequency for Gs-freqtsFrequency for Ts -printdatas"Print out the data at start of runs -progresss$Print indications of progress of runs-basefrequencysUse empirical base frequencies(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR]s< (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRXstENeighborCommandlinecBseZdZdd„ZRS(szCommandline object for the eneighbor program from EMBOSS. This is an EMBOSS wrapper around neighbor from PHYLIP. t eneighborcCsñtjj|ƒ||_tdgdgdddƒtdgdgdddƒtdgdgddd ƒtd gdgddd ƒtd gdgddd ƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgddd ƒtd!gdgddd"ƒtd#gdgddd$ƒtd%gdgddd&ƒg|_dS('Ns-infileRis infile values-outfileRsOutput file names-troutsCreate a tree files -treefilesTree file names-njsNeighbor-joinings-noogs Outgroup roots-outgnumisnumber of the outgroups -randseeds Random number seed (must be odd)s -datasetssHow many data setss -drawtrees Draw trees-ltsLower-triangular data matrixs-utsUpper-triangular data matrixs-srt Subreplicatess-randoms Randomize input order of speciess -multsetssAnalyze multiple data setss -printdatas"Print out the data at start of runs -progresss$Print indications of progress of run(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR„sH (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRstEProtParsCommandlinecBseZdZdd„ZRS(szCommandline object for the eprotpars program from EMBOSS. This is an EMBOSS wrapper around protpars from PHYLIP. t eprotparscCsKtjj|ƒ||_tdgddgdddƒtdgddgdddƒtd gdgdd d ƒtd gdgdd d ƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtd gdgdd d!ƒtd"gdgdd d#ƒtd$gdgdd d%ƒtd&gdgdd d'ƒtd(gdgdd d)ƒtd*gdgdd d+ƒtd,gddgdd d-ƒg|_dS(.Ns-msfRRisSequences file to be read ins-outfileRs Output files -besttreeisSearch for the best trees-randoms Randomize input order of speciess -norandoms'Do not randomize input order of speciess -randseeds Random number seed (must be odd)s -randtimessHow many times to randomizes-ogsUse an outgroup roots-noogsDo not use an outgroup roots-outgnumsNumber of the outgroups-threshsUse Threshold parsimonys -valthreshsthreshold values -printdatas"Print out the data at start of runs -progresss$Print indications of progress of runs-stepssPrint out steps in each sites -seqatnodess$Print sequences at all nodes of trees -drawtrees Draw trees-troutsCreate a tree files-notroutsDo not create a tree files -treefilesOutput treefile name(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR±sT (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR¬stEConsenseCommandlinecBseZdZdd„ZRS(szCommandline object for the econsense program from EMBOSS. This is an EMBOSS wrapper around consense from PHYLIP. t econsensecCs©tjj|ƒ||_tdgddgdddƒtdgddgdddƒtd gdgdd d ƒtd gdgdd d ƒtdgddgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtd gdgdd d!ƒg|_dS("Ns-infileRRis-file to read in (New Hampshire standard form)s-outfileRsOutput file names-notroutisDo not create a tree files-troutsCreate a tree files -treefilestree file names-noogsDo not use an outgroups-ogsUse an outgroups-outgnumsnumber of the outgroups -nodrawtreesDo not draw a trees -drawtrees Draw trees-rootsTrees to be treated as Rooteds -progresss(Print indications of the progress of runs -noprintsetss$Do not print out the sets of speciess -printsetssPrint out the sets of species(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRäs< (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRßstESeqBootCommandlinecBseZdZdd„ZRS(sxCommandline object for the eseqboot program from EMBOSS. This is an EMBOSS wrapper around seqboot from PHYLIP. teseqbootcCsUtjj|ƒ||_tdgddgdddƒtdgddgdddƒtd gdgddd ƒtd gdgddd ƒtd gdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒg |_dS(Ns -datafileRRis Input files-outfileRsOutput file names -randseeds Random number seed (must be odd)s-methodsChoose the methods-tests Choose tests-repssHow many replicatess-interisInterleaved inputs-enzymessPresent in input files-alls!All alleles present at each locuss -printdatas"Print out the data at start of runs -progresss$Print indications of progress of run(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR s0 (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRstWaterCommandlinecBseZdZdd„ZRS(s:Commandline object for the water program from EMBOSS. twatercCs%tjj|ƒ||_tdgddgdddƒtdgddgdddƒtdgdgddd ƒtd gdgddd ƒtd gd dgdddƒtdgddgdddƒtdgdgdddƒtdgdgdddƒtdgdgdddƒg |_dS(Ns -asequenceRRisFirst sequence to aligns -bsequencesSecond sequence to aligns-gapopensGap open penaltys -gapextendsGap extension penaltys-outfileRsOutput file for the alignments -datafileis Matrix files -similaritys'Display percent identity and similaritys -nosimilaritys.Do not display percent identity and similaritys-aformats5Display output in a different specified output format(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR*s( (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR'stFuzznucCommandlinecBseZdZdd„ZRS(s<Commandline object for the fuzznuc program from EMBOSS. tfuzznucc CsËtjj|ƒ||_tdgdgdddƒtdgdgdddƒtdgdgdddƒtd gd d gddd ƒtd gdgdddƒtdgdgdddƒg|_dS(Ns -sequenceRisSequence database USAs-patterns5Search pattern, using standard IUPAC one-letter codess -mismatchsNumber of mismatchess-outfileRRsOutput report file names -complementisSearch complementary strands-rformats'Specify the report format to output in.(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyREs (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR BstEst2GenomeCommandlinecBseZdZdd„ZRS(s?Commandline object for the est2genome program from EMBOSS. t est2genomecCstjj|ƒ||_tdgdgdddƒtdgdgdddƒtdgdd gddd ƒtd gdgdd d ƒtdgdgdd dƒtdgdgdd ddƒtdgdgdd dƒtdgdgdd ddƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dƒtdgdgdd dd ƒtd!gdgdd d"ƒtd#gdgdd d$ƒtd%gdgdd d&ƒtd'gdgdd d(ƒtd)gdgdd d*ƒtd+gdgdd d,ƒg|_dS(-Ns-estRisEST sequence(s)s-genomesGenomic sequences-outfileRRsOutput file names-matchisScore for matching two basess -mismatchsCost for mismatching two basess -gappenaltys4Cost for deleting a single base in either sequence, sexcluding intronss-intronpenaltys*Cost for an intron, independent of length.s-splicepenaltys*Cost for an intron, independent of length s+and starting/ending on donor-acceptor sitess -minscores:Exclude alignments with scores below this threshold score.s-reverses+Reverse the orientation of the EST sequences-splices$Use donor and acceptor splice sites.s-modes6This determines the comparion mode. 'both', 'forward' s 'reverse's-bests:You can print out all comparisons instead of just the bests-spacesfor linear-space recursion.s-shuffletShuffles-seedsRandom number seeds-alignsShow the alignment.s-widthsAlignment width(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRZsR (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR"WstETandemCommandlinecBseZdZdd„ZRS(s<Commandline object for the etandem program from EMBOSS. tetandemc Cstjj|ƒ||_tdgddgdddƒtdgdgdddƒtdgdgddd ƒtd gd dgddd ƒtd gdgdddƒtdgdgdddƒtdgdgdddƒtdgd gdddƒg|_dS(Ns -sequenceRRitSequences -minrepeatsMinimum repeat sizes -maxrepeatsMaximum repeat sizes-outfileRsOutput report file names -thresholdisThreshold scores -mismatchsAllow N as a mismatchs-uniformsAllow uniform consensuss-rformatsOutput report format(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR‹s$ (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR%ˆstEInvertedCommandlinecBseZdZdd„ZRS(s>Commandline object for the einverted program from EMBOSS. t einvertedc Csìtjj|ƒ||_tdgddgdddƒtdgddgdddƒtdgdgddd ƒtd gdgddd ƒtd gdgddd ƒtdgddgdddƒtdgdgdddƒg|_dS(Ns -sequenceRRiR's-gaps Gap penaltys -thresholdsMinimum score thresholds-matchs Match scores -mismatchsMismatch scores-outfileRsOutput report file names -maxrepeatis6Maximum separation between the start and end of repeat(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR¤s  (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR(¡stPalindromeCommandlinecBseZdZdd„ZRS(s?Commandline object for the palindrome program from EMBOSS. t palindromec Csétjj|ƒ||_tdgddgdddƒtdgdgdddƒtdgdgddd ƒtd gdgddd ƒtd gdgddd ƒtdgdgdddƒtdgddgdddƒg|_dS(Ns -sequenceRRiR's -minpallensMinimum palindrome lengths -maxpallensMaximum palindrome lengths -gaplimitsMaximum gap between repeatss-nummismatchessNumber of mismatches alloweds-overlapsReport overlapping matchess-outfileRsOutput report file name(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR¼s  (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR*¹stTranalignCommandlinecBseZdZdd„ZRS(s>Commandline object for the tranalign program from EMBOSS. t tranalignc Cs›tjj|ƒ||_tdgddgdddƒtdgddgdddƒtdgd dgddd ƒtd gdgdd d ƒg|_dS(Ns -asequenceRRis#Nucleotide sequences to be aligned.s -bsequencesProtein sequence alignments-outseqRsOutput sequence file.s-tableis Code to use(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRÔs (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR,ÑstDiffseqCommandlinecBseZdZdd„ZRS(s<Commandline object for the diffseq program from EMBOSS. tdiffseqc Csòtjj|ƒ||_tdgddgdddƒtdgddgdddƒtdgdgddd ƒtd gd dgddd ƒtd gd dgdddƒtdgd dgdddƒtdgd gdddƒg|_dS(Ns -asequenceRRisFirst sequence to compares -bsequencesSecond sequence to compares -wordsizes-Word size to use for comparisons (10 default)s-outfileRsOutput report file names -aoutfeats,File for output of first sequence's featuress -boutfeats-File for output of second sequence's featuress-rformatisOutput report file format(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRås  (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR.âstIepCommandlinecBseZdZdd„ZRS(sICommandline for EMBOSS iep: calculated isoelectric point and charge. tiepc CsÂtjj|ƒ||_tdgddgdddƒtdgddgdddƒtd gdgdd ƒtd gdgdd ƒtd gdgdd ƒtd gdgdd ƒg|_dS(Ns -sequenceRRisProtein sequence(s) filenames-outfileRsOutput report file names-aminois-lysinemodifieds -disulphidess -notermini(RRRR RR R (R R ((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyRýs (RRRR(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyR0úsN(RtBioRtBio.ApplicationRRRRRRRRRRR R"R%R(R*R,R.R0(((sŠ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Emboss/Applications.pyts$='-3'!1