XfRdZddlmZddlmZddlmZGddeZGddeZGd d eZGd d eZGd deZ GddeZ GddeZ GddeZ GddeZ GddeZGddeZGddeZGddeZGdd eZGd!d"eZGd#d$eZGd%d&eZGd'd(eZGd)d*eZGd+d,eZGd-d.eZGd/d0eZGd1d2eZGd3d4eZGd5d6eZGd7d8eZGd9d:eZe d;krdda#Code to interact with and run various EMBOSS programs (OBSOLETE). These classes follow the AbstractCommandline interfaces for running programs. We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly. )_Option)_Switch)AbstractCommandlineceZdZdZddZdS)_EmbossMinimalCommandLineaBase Commandline object for EMBOSS wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to all the EMBOSS tools: Attributes: - auto Turn off prompts - stdout Write standard output - filter Read standard input, write standard output - options Prompt for standard and additional values - debug Write debug output to program.dbg - verbose Report some/full command line options - help Report command line options. More information on associated and general qualifiers can be found with -help -verbose - warning Report warnings - error Report errors - fatal Report fatal errors - die Report dying program messages Nc |Jtddgdtddgdtddgd td d gd td dgdtddgdtddgdtddgdtddgdtddgdg } ||jz|_n#t$r ||_YnwxYwtj||fi|dS)Nz-autoautozTurn off prompts. Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.z-stdoutstdoutzWrite standard output.z-filterfilterz+Read standard input, write standard output.z-optionsoptionszPrompt for standard and additional values. If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.z-debugdebugz"Write debug output to program.dbg.z-verboseverbosez%Report some/full command line optionsz-helphelpztReport command line options. More information on associated and general qualifiers can be found with -help -verbosez-warningwarningzReport warnings.z-errorerrorzReport errors.z-diediezReport dying program messages.)r parametersAttributeErrorr__init__selfcmdkwargsextra_parameterss 7lib/python3.11/site-packages/Bio/Emboss/Applications.pyrz"_EmbossMinimalCommandLine.__init__/sS &!T   Y)+C D D H%'T   Y'9   Xw')M N N Z+-T U U &!3   Z+-? @ @ Xw')9 : : VUO%E F F7 : //@DOO / / /.DOOO / $T399&99999s2CCCN__name__ __module__ __qualname____doc__rrrrs2,&:&:&:&:&:&:r#rc eZdZdZddZdZdS)_EmbossCommandLinezBase Commandline object for EMBOSS wrappers (PRIVATE). This is provided for subclassing, it deals with shared options common to all the EMBOSS tools plus: - outfile Output filename Nc |Jtddgddg} ||jz|_n#t$r ||_YnwxYwtj||fi|dS)Nz-outfileoutfilezOutput filenameTfilename)rrrrrrs rrz_EmbossCommandLine.__init__bs Z+-> N N N  //@DOO / / /.DOOO / "*4???????s +??c~|js|js|jstdt|S)N]You must either set outfile (output filename), or enable filter or stdout (output to stdout).)r'r r ValueErrorr _validaters rr-z_EmbossCommandLine._validatepsN    t{ A )224888r#rrrr r!rr-r"r#rr%r%XsE @ @ @ @ 9 9 9 9 9r#r%ceZdZdZddZdS)Primer3CommandlineaCommandline object for the Primer3 interface from EMBOSS. The precise set of supported arguments depends on your version of EMBOSS. This version accepts arguments current at EMBOSS 6.1.0: >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True) >>> cline.explainflag = True >>> cline.osizeopt=20 >>> cline.psizeopt=200 >>> cline.outfile = "myresults.out" >>> cline.bogusparameter = 1967 # Invalid parameter Traceback (most recent call last): ... ValueError: Option name bogusparameter was not found. >>> print(cline) eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True eprimer3c Fgtddgddtddgdtd d gd td d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,td-d.gd/td0d1gd2td3d4gd5td6d7gd8td9d:gd;tdtd?d@gdAtdBdCgdDtdEdFgdGtdHdIgdJtdKdLgdMtdNdOgdPtdQdRgdStdTdUgdVtdWdXgdYtdZd[gd\td]d^gd_td`dagdbtdcddgdetdfdggdhtdidjgdktdldmgdntdodpgdqtdrdsgdttdudvgdwtdxdygdztd{d|gd}td~dgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgd|_tj||fi|dS)Initialize the class. -sequencesequencez Sequence to choose primers from.T is_requiredz-tasktaskz#Tell eprimer3 what task to perform.z -hybridprobe hybridprobez-Find an internal oligo to use as a hyb probe.z -numreturn numreturnz)Maximum number of primer pairs to return.z-includedregionincludedregionz3Subregion of the sequence in which to pick primers.z-targettargetz(Sequence to target for flanking primers.z-excludedregionexcludedregionz'Regions to exclude from primer picking.z -forwardinput forwardinputz&Sequence of a forward primer to check.z -reverseinput reverseinputz&Sequence of a reverse primer to check.z-gcclampgcclampz:The required number of Gs and Cs at the 3' of each primer.z-osizeosizez!Optimum length of a primer oligo.z-minsizeminsizez!Minimum length of a primer oligo.z-maxsizemaxsizez!Maximum length of a primer oligo.z-otmotmz[Melting temperature for primer oligo (OBSOLETE). Option replaced in EMBOSS 6.6.0 by -opttmz-opttmopttmz]Optimum melting temperature for a primer oligo. Option added in EMBOSS 6.6.0, replacing -otmz-mintmmintmz/Minimum melting temperature for a primer oligo.z-maxtmmaxtmz/Maximum melting temperature for a primer oligo.z -maxdifftm maxdifftmzOMaximum difference in melting temperatures between forward and reverse primers.z -ogcpercent ogcpercentzOptimum GC% for a primer.z-mingcmingczMinimum GC% for a primer.z-maxgcmaxgczMaximum GC% for a primer.z -saltconcsaltconcz)Millimolar salt concentration in the PCR.z-dnaconcdnaconcz7Nanomolar concentration of annealing oligos in the PCR.z -maxpolyxmaxpolyxz;Maximum allowable mononucleotide repeat length in a primer.z -psizeoptpsizeoptz!Optimum size for the PCR product.z-prangeprangez/Acceptable range of length for the PCR product.z-ptmoptptmoptz0Optimum melting temperature for the PCR product.z-ptmminptmminz5Minimum allowed melting temperature for the amplicon.z-ptmmaxptmmaxz5Maximum allowed melting temperature for the amplicon.z-oexcludedregionoexcludedregionz+Do not pick internal oligos in this region.z -oligoinput oligoinputzSequence of the internal oligo.z -osizeoptosizeoptz!Optimum length of internal oligo.z -ominsizeominsizez!Minimum length of internal oligo.z -omaxsizeomaxsizez!Maximum length of internal oligo.z-otmoptotmoptz.Optimum melting temperature of internal oligo.z-otmminotmminz.Minimum melting temperature of internal oligo.z-otmmaxotmmaxz.Maximum melting temperature of internal oligo.z-ogcoptogcoptzOptimum GC% for internal oligo.z-ogcminogcminzMinimum GC% for internal oligo.z-ogcmaxogcmaxzMaximum GC% for internal oligo.z -osaltconc osaltconcz6Millimolar concentration of salt in the hybridisation.z -odnaconcodnaconcz?Nanomolar concentration of internal oligo in the hybridisation.z -oanyselfoanyselfz;Maximum allowable alignment score for self-complementarity.z -oendselfoendselfz Y'L  ?_ F Xw')L M MG_ H Z+-P Q QI_ J Z+-P Q QK_ L <  M_ V 7#?  W_ ` 7#%V  a_ f 7#%V  g_ l {+/  m_ v ]L13N O Ow_ x Xw')D E Ey_ z Xw')D E E{_ | j)+V  }_ B Y'I  C_ J j)M  K_ T [*-/R S SU_ V H%'X  W_ ^ H%B  __ f H%G  g_ n H%G  o_ x #%67=  y_ @ ]L13T U UA_ D [*-/R S SE_ F [*-/R S SG_ H [*-/R S SI_ L H%'W  M_ R H%'W  S_ X H%'W  Y_ ` Y)+L M Ma_ b Y)+L M Mc_ d Y)+L M Me_ h {+H  i_ p j)Q  q_ z j)M  {_ B j)N  C_ J {+L  K_ R )+BCJ  S_ Z !?3:  [_ d  -;  e_ n %':;M  o_ v />  w_ @ #D#8888888r#N)r2rr"r#rr1r1|s8&b9b9b9b9b9b9r#r1ceZdZdZddZdS)PrimerSearchCommandlinez 0.001)z -invarfrac invarfraczproportoin of invariant sites-ttratiottratioz ts/tv ratioz -freqsfrom freqsfromzuse empirical base freqs -basefreqbasefreqzspecify basefreqsz-lowerlowerzlower triangle matrix (y/N)Nrjrks rrzFDNADistCommandline.__init__`sL j)*     Y)+CQU V V V Xw')9 : : ^]35V W W Wf%'? @ @  -/U   Z+^ < < $&89;V   \;/1P Q Q Z+] ; ; \;/1K L L [*-/B C C Xw')F G G- 0 #D#8888888r#N)r~rr"r#rr}r}Ys2 999999r#r}ceZdZdZddZdS)FTreeDistCommandlinezCommandline object for the ftreedist program from EMBOSS. ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for calculating distance measures between phylogentic trees. ftreedistc tddgdddtddgdtd d gd td d gdtddgdtddgdg|_tj||fi|dS)r4 -intreefile intreefileztree file to score (phylip)Trtz-dtypedtypez*distance type ([S]ymetric, [b]ranch score)z-pairingpairingz   [*-/G H H Z+-A B B Y)+I J J Wf%'> ? ? Xw'); < < ^]35O P P [*-/E F F \;/1C D D% ( #D#8888888r#N)rrr"r#rrrs2 999999r#rceZdZdZddZdS)FSeqBootCommandlinezCommandline object for the fseqboot program from EMBOSS. fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to pseudo-sample alignment files. fseqbootc tddgdddtddgdtd d gd td d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&td'd(gd)g |_tj||fi|d*S)+r4r5r6zseq file to sample (phylip)Trtr catergorieszfile of input categoriesrrz weights filez-testtestz'specify operation, default is bootstrapz-regularregularzabsolute number to resamplez -fracsample fracsamplezfraction to resamplez-rewriteformat rewriteformatz'output format ([P]hyilp, [n]exus, [x]mlz-seqtypeseqtypez&output format ([D]na, [p]rotein, [r]naz -blocksize blocksizerz-repsrepsz%how many replicates, defaults to 100)z -justweights jusweightsz.what to write out [D]atasets of just [w]eightsrrzspecify random seed-dotdiffdotdiffUse dot-differencing? [Y/n]Nrjrks rrzFSeqBootCommandline.__init__sF j)-     ]M24N O O Z+_ = = Wf%'P Q Q Z+-J K K ]L13I J J !?39   Z+-U V V \;/1G H H Wf%'N O O .@   Wf%'< = = Z+-J K K1 4 #D#8888888r#N)rrr"r#rrrs2 999999r#rceZdZdZddZdS)FDNAParsCommandlineaCommandline object for the fdnapars program from EMBOSS. fdnapars is an EMBOSS version of the PHYLIP program dnapars, for estimating trees from DNA sequences using parsiomny. Calling this command without providing a value for the option "-intreefile" will invoke "interactive mode" (and as a result fail if called with subprocess) if "-auto" is not set to true. fdnaparsc >tddgdddtddgdtd d gd td d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,td-d.gd/g|_tj||fi|d0S)1r4r5r6rTrtrrzPhylip tree filerrrz -maxtreesmaxtreeszmax trees to save during runz -thoroughthoroughzmore thorough search (Y/n)z -rearrange rearrangez#Rearrange on just 1 best tree (Y/n)z -transversion transversionzUse tranversion parsimony (y/N)-njumblenjumble7number of times to randomise input order (default is 0)rrprovide random seedrrSpecify outgroup-threshthreshUse threshold parsimony (y/N) -threshold thresholdThreshold valuerrWrite trees to file (Y/n)rrrrrrNrjrks rrzFDNAParsCommandline.__init__sl j)*     ]L13E F F Z+^ < < [*-/M N N [*-/K L L \;/1V W W  .13T   Y'I   Wf%'< = = Z+-? @ @ Y)+J K K \;/1B C C Xw')D E E ^]35O P P Z+-J K K3 6 #D#8888888r#N)rrr"r#rrr2999999r#rceZdZdZddZdS)FProtParsCommandlineaCommandline object for the fdnapars program from EMBOSS. fprotpars is an EMBOSS version of the PHYLIP program protpars, for estimating trees from protein sequences using parsiomny. Calling this command without providing a value for the option "-intreefile" will invoke "interactive mode" (and as a result fail if called with subprocess) if "-auto" is not set to true. fprotparsc tddgdddtddgdtd d gd ddtd d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&g |_tj||fi|d'S)(r4r5r6rTrtrrzPhylip tree file to scorerrzphylip tree output filerrr -whichcode whichcodez which genetic code, [U,M,V,F,Y]]rrrrrrrrrrrrrrrrrrrrrNrjrks rrzFProtParsCommandline.__init__s> j)*     ]L13N O O /)     Z+^ < < \;/1S T T Y'I   Wf%'< = = Z+-? @ @ Y)+J K K \;/1B C C Xw')D E E Z+-J K K3 6 #D#8888888r#N)rrr"r#rrr rr#rceZdZdZddZdS)FProtDistCommandlinezCommandline object for the fprotdist program from EMBOSS. fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to estimate trees from protein sequences using parsimony fprotdistc tddgdddtddgdtd d gd td d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,g|_tj||fi|d-S).r4r5r6rTrtrrrrrrz -catergoriesrz file of ratesrrrrrzsub. model [j,h,d,k,s,c]rrzgamma [g, i,c]rrrz-invarcoefficientinvarcoefficientz4float for variation of substitution rate among sitesz-aacategaacategz"Choose the category to use [G,C,H]rrzgenetic code [c,m,v,f,y]z-easeeasez,Pob change category (float between -0 and 1)rrz#Transition/transversion ratio (0-1)rrz+DNA base frequencies (space separated list)Nrjrks rrzFProtDistCommandline.__init__=s_ j)*     ^]35V W W Wf%'? @ @ ^]3_ E E Z+^ < < Y)+E F F Xw')9 : : $&89;V   $&89F   Z+-Q R R \;/1K L L Wf%'U V V Z+-R S S j)+X  1 8 #D#8888888r#N)rrr"r#rrr6s2 999999r#rceZdZdZddZdS)FConsenseCommandlinezCommandline object for the fconsense program from EMBOSS. fconsense is an EMBOSS wrapper for the PHYLIP program consense used to calculate consensus trees. fconsensec .tddgdddtddgdtd d gd td d gdtddgdtddgdtddgdg|_tj||fi|dS)r4rrz-file with phylip trees to make consensus fromTrtrrz!consensus method [s, mr, MRE, ml]z-mlfracmlfracz8cut-off freq for branch to appear in consensus (0.5-1.0)z-rootrootztreat trees as rooted (YES, no)rrz&OTU to use as outgroup (starts from 0)rrrrz"Phylip tree output file (optional)Nrjrks rrzFConsenseCommandline.__init__es  -?     Y)+N O O H%J   Wf%'H I I Z+-U V V Xw')J K K /1U   & #D#8888888r#N)rrr"r#rrr^rr#rceZdZdZddZdS)WaterCommandlinez5Commandline object for the water program from EMBOSS.waterc tddgdddtddgdddtd d gd d td dgdd tddgddtddgdtddgdtddgdtddgdtd d!gd"td#d$gd%g |_tj||fi|d&S)'r4 -asequence asequenceFirst sequence to alignTrt -bsequence bsequenceSecond sequence to align-gapopengapopenGap open penaltyr7 -gapextend gapextendGap extension penaltyrr Matrix filer(-nobriefnobrief(Display extended identity and similarity-briefbrief%Display brief identity and similarity -similarity similarity'Display percent identity and similarityrvrwrxryrzr{-aformataformat5Display output in a different specified output formatNrrrr%rrks rrzWaterCommandline.__init__sX {+)     {+*     Z+-?T R R R {+-DRV    [*-}t L L L Y')S   Xw')P Q Q  -/X   /1U   [*-/P Q Q Y'G  ;! D #D#8888888r#N)rrr"r#rrr}s.??$9$9$9$9$9$9r#rceZdZdZddZdS)NeedleCommandlinez6Commandline object for the needle program from EMBOSS.needlec .tddgdddtddgdddtd d gd d td dgdd tddgddtddgdtddgdtddgdtddgdtd d!gd"td#d$gd%td&d'gd(td)d*gd+td,d-gd.g|_tj||fi|d/S)0r4rrrTrtrrrrrrr7rrrrrrr( -endweight endweightApply And gap penalties-endopenendopen0The score taken away when an end gap is created. -endextend endextendOThe score added to the end gap penalty for each base or residue in the end gap.rrrrrrr r r rvrwrxryrzr{r r rNrrks rrzNeedleCommandline.__init__s {+)     {+*     Z+-?T R R R {+-DRV    [*-}t L L L \;/1J K K Y'B   {+*   Y')S   Xw')P Q Q  -/X   /1U   [*-/P Q Q Y'G  O+ X #D#8888888r#N)rrr"r#rrrs.@@.9.9.9.9.9.9r#rceZdZdZddZdS)NeedleallCommandlinez9Commandline object for the needleall program from EMBOSS. needleallc rtddgdddtddgdddtd d gd d td dgdd tddgddtddgdtddgdtddgdtddgdtd d!gd"td#d$gd%td&d'gd(td)d*gd+td,d-gd.td/d0gd1td2d3gd4g|_tj||fi|d5S)6r4rrrTrtrrrrrrr7rrrrrrr( -minscoreminscore:Exclude alignments with scores below this threshold score.z -errorfile errorfilezError file to be written to.rrrrrrrrrrrrrrrr r r rvrwrxryrzr{r r rNrrks rrzNeedleallCommandline.__init__s {+)     {+*     Z+-?T R R R {+-DRV    [*-}t L L L j)L   \;/1O P P \;/1J K K Y'B   {+*   Y')S   Xw')P Q Q  -/X   /1U   [*-/P Q Q Y'G  Y0 b #D#8888888r#N)rrr"r#rrrs.CC393939393939r#rceZdZdZddZdS)StretcherCommandlinez9Commandline object for the stretcher program from EMBOSS. stretcherc jtddgdddtddgdddtd d gd dd tddgddd tddgddtddgdtddgdtddgdg|_tj||fi|dS) r4rrrTrtrrrrrrc,t|tSr isinstanceintvalues rz/StretcherCommandline.__init__..*z%/E/Er#)r8checker_functionrrrc,t|tSrr*r-s rr/z/StretcherCommandline.__init__..0r0r#rrrr(rvrwrxryrzr{r r rNrjrks rrzStretcherCommandline.__init__s' {+)     {+*     Y'" !E!E     {+' !E!E     [*-}t L L L /1U   [*-/P Q Q Y'G  =" F #D#8888888r#N)r'rr"r#rr&r&s.CC%9%9%9%9%9%9r#r&ceZdZdZddZdS)FuzznucCommandlinez7Commandline object for the fuzznuc program from EMBOSS.fuzznucc tddgddtddgddtd d gd td d gdtddgdg|_tj||fi|dS)r4r5r6Sequence database USATr7-patternpattern5Search pattern, using standard IUPAC one-letter codes -pmismatch pmismatchNumber of mismatchesz -complement complementzSearch complementary strand-rformatrformat'Specify the report format to output in.Nrjrks rrzFuzznucCommandline.__init__Bs j)+BPT    Y'G     \;/1G H H ]L13P Q Q Z+-V W W   #D#8888888r#N)r5rr"r#rr4r4?s.AA999999r#r4ceZdZdZddZdS)FuzzproCommandlinez7Commandline object for the fuzzpro program from EMBOSS.fuzzproc tddgddtddgddtd d gd td d gdg|_tj||fi|dS)r4r5r6r7Tr7r8r9r:r;r<r=r?r@rANrjrks rrzFuzzproCommandline.__init__Ws j)+BPT    Y'G     \;/1G H H Z+-V W W   #D#8888888r#N)rDrr"r#rrCrCTs.AA999999r#rCceZdZdZddZdS)Est2GenomeCommandlinez:Commandline object for the est2genome program from EMBOSS. est2genomec tddgddtddgddtd d gd td d gdtddgdtddgdtddgdtddgdtddgdtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,td-d.gd/td0d1gd2td3d4gd5g|_tj||fi|d6S)7r4z-estestzEST sequence(s)Tr7z-genomegenomezGenomic sequence-matchmatchzScore for matching two bases -mismatchmismatchzCost for mismatching two basesz -gappenalty gappenaltyzECost for deleting a single base in either sequence, excluding intronsz-intronpenalty intronpenaltyz*Cost for an intron, independent of length.z-splicepenalty splicepenaltyzUCost for an intron, independent of length and starting/ending on donor-acceptor sitesr!r"r#z-reversereversez+Reverse the orientation of the EST sequencez-splicesplicez$Use donor and acceptor splice sites.z-modemodezDThis determines the comparison mode. 'both', 'forward', or 'reverse'z-bestbestz:You can print out all comparisons instead of just the bestz-spacespacezfor linear-space recursion.z-shuffleshuffleShufflerrzRandom number seedz-alignalignzShow the alignment.z-widthwidthzAlignment widthNrjrks rrzEst2GenomeCommandline.__init__ks VUO%6D I I I Y)+=4 P P P Xw')G H H [*-/O P P  -$   !?3<   !?3>   j)L   Y')V   Y)+Q R R &!V   &!L   Xw')F G G Z+Y 7 7 Wf%'; < < Xw')> ? ? Xw'): ; ;O( R #D#8888888r#N)rHrr"r#rrGrGhs.DD+9+9+9+9+9+9r#rGceZdZdZddZdS)ETandemCommandlinez7Commandline object for the etandem program from EMBOSS.etandemc 6tddgdddtddgdd td d gd d td dgdtddgdtddgdtddgdg|_tj||fi|dS)r4r5r6SequenceTrtz -minrepeat minrepeatzMinimum repeat sizer7 -maxrepeat maxrepeatzMaximum repeat sizerrzThreshold scorerNrOzAllow N as a mismatchz-uniformuniformzAllow uniform consensusr?r@zOutput report formatNrjrks rrzETandemCommandline.__init__s j):RV    {+-BPT    {+-BPT    \;/1B C C [*-/F G G Z+-F G G Z+-C D D  #D#8888888r#N)r^rr"r#rr]r]s.AA999999r#r]ceZdZdZddZdS)EInvertedCommandlinez9Commandline object for the einverted program from EMBOSS. einvertedc tddgdddtddgdddtd d gd d td dgdd tddgdd tddgdg|_tj||fi|dS)r4r5r6r`Trtz-gapgapz Gap penaltyrrzMinimum score thresholdr7rLrMz Match scorerNrOzMismatch scorerbrcz6Maximum separation between the start and end of repeatNrjrks rrzEInvertedCommandline.__init__s j):RV    VUO]Tt T T T {+-FTX    Xw'D I I I [*-/?T R R R {+H    #D#8888888r#N)rgrr"r#rrfrfs.CC999999r#rfceZdZdZddZdS)PalindromeCommandlinez:Commandline object for the palindrome program from EMBOSS. palindromec tddgdddtddgdd td d gd d td dgdd tddgdd tddgdd g|_tj||fi|dS)r4r5r6r`Trtz -minpallen minpallenzMinimum palindrome lengthr7z -maxpallen maxpallenzMaximum palindrome lengthz -gaplimitgaplimitzMaximum gap between repeatsz-nummismatches nummismatcheszNumber of mismatches allowedz-overlapoverlapzReport overlapping matchesNrjrks rrzPalindromeCommandline.__init__s j):RV    {++     {++     j)-     !?3.     Y')ESW   1 8 #D#8888888r#N)rlrr"r#rrkrks.DD999999r#rkceZdZdZddZdS)TranalignCommandlinez9Commandline object for the tranalign program from EMBOSS. tranalignc tddgdddtddgdddtd d gd ddtd d gdg|_tj||fi|dS)r4rrz#Nucleotide sequences to be aligned.TrtrrzProtein sequence alignment-outseqoutseqOutput sequence file.z-tabletablez Code to useNrjrks rrzTranalignCommandline.__init__s {+5     {+,     H%'     Xw' 7 7' * #D#8888888r#N)rurr"r#rrtrts.CC999999r#rtceZdZdZddZdS)DiffseqCommandlinez7Commandline object for the diffseq program from EMBOSS.diffseqc "tddgdddtddgdddtd d gd d td dgdddtddgdddtddgdg|_tj||fi|dS)r4rrzFirst sequence to compareTrtrrzSecond sequence to compare -wordsizewordsizez-Word size to use for comparisons (10 default)r7z -aoutfeataoutfeatz,File for output of first sequence's featuresz -boutfeatboutfeatz-File for output of second sequence's featuresr?r@zOutput report file formatNrjrks rrzDiffseqCommandline.__init__ s {++     {+,     j)?     j)>     j)?     Z+-H I I= @ #D#8888888r#N)r}rr"r#rr|r|s.AA"9"9"9"9"9"9r#r|ceZdZdZddZdS)IepCommandlineaCommandline for EMBOSS iep: calculated isoelectric point and charge. Examples -------- >>> from Bio.Emboss.Applications import IepCommandline >>> iep_cline = IepCommandline(sequence="proteins.faa", ... outfile="proteins.txt") >>> print(iep_cline) iep -outfile=proteins.txt -sequence=proteins.faa You would typically run the command line with iep_cline() or via the Python subprocess module, as described in the Biopython tutorial. iepc tddgdddtddgdtd d gd td d gdtddgdtddgdg|_tj||fi|dS)r4r5r6zProtein sequence(s) filenameTrtz-aminoaminozZNumber of N-termini Integer 0 (default) or more. z -carboxylcarboxylzZNumber of C-termini Integer 0 (default) or more. z-lysinemodifiedlysinemodifiedzaNumber of modified lysines Integer 0 (default) or more. z -disulphides disulphideszcNumber of disulphide bridges Integer 0 (default) or more. z -notermini noterminiz=Exclude (True) or include (False) charge at N and C terminus.Nrjrks rrzIepCommandline.__init__@s j).     7#   j)   "$45   /   {+O  I( R #D#8888888r#N)rrr"r#rrr0s2  +9+9+9+9+9+9r#rc eZdZdZddZdZdS)SeqretCommandlineaCommandline object for the seqret program from EMBOSS. This tool allows you to interconvert between different sequence file formats (e.g. GenBank to FASTA). Combining Biopython's Bio.SeqIO module with seqret using a suitable intermediate file format can allow you to read/write to an even wider range of file formats. This wrapper currently only supports the core functionality, things like feature tables (in EMBOSS 6.1.0 onwards) are not yet included. seqretc tddgddtddgddtd d gd td d gdg|_tj||fi|dS)r4r5r6zInput sequence(s) filenameTr(rwrxryz-sformatsformatz.Input sequence(s) format (e.g. fasta, genbank)z -osformatosformatz/Output sequence(s) format (e.g. fasta, genbank)N)rrrrrks rrzSeqretCommandline.__init__{s j)+GRV    Y)+BT R R R Y'@   j)A     "*4???????r#c|js|js|jstd|js|js|jstdt |S)Nr+z\You must either set sequence (input filename), or enable filter or stdin (input from stdin).)rxr r r,r6stdintrr-r.s rr-zSeqretCommandline._validates  t{ dk A      @ )224888r#N)rr/r"r#rrrosE  @@@@$99999r#rceZdZdZddZdS)SeqmatchallCommandlineakCommandline object for the seqmatchall program from EMBOSS. e.g. >>> cline = SeqmatchallCommandline(sequence="opuntia.fasta", outfile="opuntia.txt") >>> cline.auto = True >>> cline.wordsize = 18 >>> cline.aformat = "pair" >>> print(cline) seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair seqmatchallc tddgdddtddgdtd d gd g|_tj||fi|d S) r4r5r6zReadable set of sequencesTrtrrz(Word size (Integer 2 or more, default 4)r r rNrjrks rrzSeqmatchallCommandline.__init__s j)+     j)+U   Y'G    #D#8888888r#N)rrr"r#rrrs2  999999r#r__main__) run_doctestN)#r!Bio.Applicationrrrrr%r1rmr}rrrrrrrrrrr&r4rCrGr]rfrkrtr|rrrr Bio._utilsrr"r#rrs"$###########//////=:=:=:=:=: 3=:=:=:@!9!9!9!9!92!9!9!9Hv9v9v9v9v9+v9v9v9r!9!9!9!9!90!9!9!9H!9!9!9!9!9,!9!9!9H99999-999>99999-999@#9#9#9#9#9,#9#9#9L'9'9'9'9'9,'9'9'9T'9'9'9'9'9-'9'9'9T%9%9%9%9%9-%9%9%9P99999-999>'9'9'9'9'9)'9'9'9T1919191919*191919h6969696969-696969r(9(9(9(9(9-(9(9(9V99999+999*99999+999(.9.9.9.9.9..9.9.9b99999+999.99999-999.!9!9!9!9!9.!9!9!9H99999-999:%9%9%9%9%9+%9%9%9P;9;9;9;9;9';9;9;9~,9,9,9,9,91,9,9,9^99999/999B z&&&&&&KMMMMMr#