o RŀgYN@sbdZddlZddlmZddlmZddlmZGdddeZedkr/dd lm Z e dSdS) zBCommand line wrapper for the multiple alignment program Clustal W.N)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)ClustalwCommandlineaSCommand line wrapper for clustalw (version one or two). http://www.clustal.org/ Notes ----- Last checked against versions: 1.83 and 2.1 References ---------- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. Examples -------- >>> from Bio.Align.Applications import ClustalwCommandline >>> in_file = "unaligned.fasta" >>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file) >>> print(clustalw_cline) clustalw2 -infile=unaligned.fasta You would typically run the command line with clustalw_cline() or via the Python subprocess module, as described in the Biopython tutorial. clustalwcKsgtgddddtgddddtgddddtgdd tgd d tgd d tgd dtgddtgddtgddtgdddddtgddtgddtgddd ddtgd!d"tgd#d$ddtgd%d&d'ddtgd(d)d*ddtgd+d,d-ddtgd.d/d0ddtgd1d2d3ddtgd4d5tgd6d7d8ddtgd9d:tgd;dd?ddtgd@dAdBddtgdCdDdEddtgdFdGdHddtgdIdJdKddtgdLdMdNdddOtgdPdQdRdddOtgdSdTdUddtgdVdWdXddtgdYdZddtgd[d\d]dddOtgd^dMd_dddOtgd`dQdadddOtgdbdTdcddtgdddWdeddtgdfdgtgdhdidjddtgdkdltgdmdntgdodptgdqdrdsddtgdtdudvddtgdwdxdyddtgdzd{d|ddtgd}d~tgddtgddddtgddddtgddddddOtgddddddOtgddtgddtgddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgdddddtgddtgddtgdddddtgddddd|_tj||fi|dS)zInitialize the class.)z-infilez-INFILEINFILEinfilezInput sequences.T)filename)z -profile1z -PROFILE1PROFILE1profile1zProfiles (old alignment).)z -profile2z -PROFILE2PROFILE2profile2)z-optionsz-OPTIONSOPTIONSoptionsz List the command line parameters)z-helpz-HELPHELPhelpz Outline the command line params.)z-checkz-CHECKCHECKcheck)z -fullhelpz -FULLHELPFULLHELPfullhelpzOutput full help content.)z-alignz-ALIGNALIGNalignzDo full multiple alignment.)z-treez-TREETREEtreezCalculate NJ tree.)z-pimz-PIMPIMpimz[ z.ClustalwCommandline.__init__..)checker_function)z-convertz-CONVERTCONVERTconvertz6Output the input sequences in a different file format.)z -quicktreez -QUICKTREE QUICKTREE quicktreez/Use FAST algorithm for the alignment guide tree)z-typez-TYPETYPEtypezPROTEIN or DNA sequencescS|dvS)N)PROTEINDNAproteindnar%r#r%r%r&r'q)z -negativez -NEGATIVENEGATIVEnegativez0Protein alignment with negative values in matrix)z-outfilez-OUTFILEOUTFILEoutfilez#Output sequence alignment file name)z-outputz-OUTPUTOUTPUToutputzGOutput format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTAcSr0)N)CLUSTALGCGGDEPHYLIPPIRNEXUSFASTAclustalgcggdephylippirnexusfastar%r#r%r%r&r')z -outorderz -OUTORDEROUTORDERoutorderz$Output taxon order: INPUT or ALIGNEDcSr0)N)INPUTinputALIGNEDalignedr%r#r%r%r&r'rJ)z-casez-CASECASEcasez$LOWER or UPPER (for GDE output only)cSr0)N)UPPERupperLOWERlowerr%r#r%r%r&r'r5)z-seqnosz-SEQNOSSEQNOSseqnosz#OFF or ON (for Clustal output only)cSr0N)ONonOFFoffr%r#r%r%r&r'r5)z -seqno_rangez -SEQNO_RANGE SEQNO_RANGE seqno_rangez'OFF or ON (NEW- for all output formats)cSr0rYr%r#r%r%r&r'r5)z-rangez-RANGERANGErangezGSequence range to write starting m to m+n. Input as string eg. 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