o RŀgM@sfdZddlmZddlmZddlmZddlmZGdddeZedkr1dd lm Z e d Sd S) z@Command line wrapper for the multiple alignment programme MAFFT.) _Argument)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)MafftCommandlinea Command line wrapper for the multiple alignment program MAFFT. http://align.bmr.kyushu-u.ac.jp/mafft/software/ Notes ----- Last checked against version: MAFFT v6.717b (2009/12/03) References ---------- Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (describes RNA structural alignment methods) Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent developments in the MAFFT multiple sequence alignment program (outlines version 6) Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm) Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) Katoh, Misawa, Kuma, Miyata (Nucleic Acids Res. 30:3059-3066, 2002) Examples -------- >>> from Bio.Align.Applications import MafftCommandline >>> mafft_exe = "/opt/local/mafft" >>> in_file = "../Doc/examples/opuntia.fasta" >>> mafft_cline = MafftCommandline(mafft_exe, input=in_file) >>> print(mafft_cline) /opt/local/mafft ../Doc/examples/opuntia.fasta If the mafft binary is on the path (typically the case on a Unix style operating system) then you don't need to supply the executable location: >>> from Bio.Align.Applications import MafftCommandline >>> in_file = "../Doc/examples/opuntia.fasta" >>> mafft_cline = MafftCommandline(input=in_file) >>> print(mafft_cline) mafft ../Doc/examples/opuntia.fasta You would typically run the command line with mafft_cline() or via the Python subprocess module, as described in the Biopython tutorial. Note that MAFFT will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:: stdout, stderr = mafft_cline() with open("aligned.fasta", "w") as handle: handle.write(stdout) from Bio import AlignIO align = AlignIO.read("aligned.fasta", "fasta") Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:: stdout, stderr = mafft_cline() from io import StringIO from Bio import AlignIO align = AlignIO.read(StringIO(stdout), "fasta") mafftc sHgdgtddgdtgddtddgd td d gd td dgdtddgdtddgdddddtddgdddddtddgd d!dddtd"d#gd$d%dddtd&d'gd(td)d*gd+td,d-gd.td/d0gd1td2d3gd4td5d6gd7td8d9gd:td;ddddtd?d@gdAtdBdCgdDtdEdFgdGtdHdIgdJdKdddtdLdMgdNdOdddtdPdQgdRdSdddtdTdUgdVdWdddtdXdYgdZd[dddtd\d]gd^d_dddtd`dagdbdcdddtdddegdffdgdddtdhdigdjddktdldmgdndoddptdqdrgdsdoddptdtdugdvtdwdxgdydzdddtd{d|gd}td~dgdtddgdtddgdtddgdtddgdtddgdtddgdtddgddoddptdgddododtdgddod|_tj||fi|dS)zInitialize the class.)30456280z--autoautoz+Automatically select strategy. Default off.)z --6merpair6merpair sixmerpairzGDistance is calculated based on the number of shared 6mers. Default: onz --globalpair globalpairzVAll pairwise alignments are computed with the Needleman-Wunsch algorithm. Default: offz --localpair localpairzTAll pairwise alignments are computed with the Smith-Waterman algorithm. Default: offz --genafpair genafpairz~All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). Default: offz --fastapair fastapairzWAll pairwise alignments are computed with FASTA (Pearson and Lipman 1988). Default: offz --weightiweightiz[Weighting factor for the consistency term calculated from pairwise alignments. Default: 2.7cS t|tSN isinstancefloatxrQ/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_Mafft.py z+MafftCommandline.__init__..F)checker_functionequatez--retreeretreez_Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2cSrrrintrrrrrrz --maxiterate maxiteratez?Number cycles of iterative refinement are performed. Default: 0cSrrr"rrrrrrz--threadthreadz$Number of threads to use. Default: 1cSrrr"rrrrrrz--fftfftz>Use FFT approximation in group-to-group alignment. Default: onz--nofftnofftzFDo not use FFT approximation in group-to-group alignment. Default: offz --noscorenoscorezaAlignment score is not checked in the iterative refinement stage. Default: off (score is checked)z --memsavememsavezyUse the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).z --parttreeparttreezDUse a fast tree-building method with the 6mer distance. Default: offz --dpparttree dpparttreezGThe PartTree algorithm is used with distances based on DP. Default: offz--fastaparttree fastaparttreezJThe PartTree algorithm is used with distances based on FASTA. Default: offz --partsizepartsizez?The number of partitions in the PartTree algorithm. Default: 50cSrrr"rrrrrrz --groupsize groupsizezZDo not make alignment larger than number sequences. Default: the number of input sequencesz--adjustdirectionadjustdirectionz>Adjust direction according to the first sequence. Default off.z--adjustdirectionaccuratelyadjustdirectionaccuratelyz`Adjust direction according to the first sequence,for highly diverged data; very slowDefault off.z--opopz>Gap opening penalty at group-to-group alignment. Default: 1.53cSrrrrrrrrrz--epepzcOffset value, which works like gap extension penalty, for group-to- group alignment. Default: 0.123cSrrrrrrrr rz--loplopz?Gap opening penalty at local pairwise alignment. Default: 0.123cSrrrrrrrrrz--leplepz6Offset value at local pairwise alignment. Default: 0.1cSrrrrrrrrrz--lexplexpz@Gap extension penalty at local pairwise alignment. Default: -0.1cSrrrrrrrr"rz--LOPLOPz9Gap opening penalty to skip the alignment. Default: -6.00cSrrrrrrrr*rz--LEXPLEXPz:Gap extension penalty to skip the alignment. Default: 0.00cSrrrrrrrr2rz--blblz)BLOSUM number matrix is used. Default: 62cs|vSrrrBLOSUM_MATRICESrrr:sz--jttjttzNJTT PAM number (Jones et al. 1992) matrix is used. number>0. Default: BLOSUM62)r z--tmtmzXTransmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62T)filenamer z --aamatrixaamatrixz7Use a user-defined AA scoring matrix. Default: BLOSUM62z--fmodelfmodelzeIncorporate the AA/nuc composition information into the scoring matrix (True) or not (False, default)z --namelength namelengthaWName length in CLUSTAL and PHYLIP output. MAFFT v6.847 (2011) added --namelength for use with the --clustalout option for CLUSTAL output. MAFFT v7.024 (2013) added support for this with the --phylipout option for PHYLIP output (default 10). cSrrr"rrrrrjrz --clustalout clustaloutz7Output format: clustal (True) or fasta (False, default)z --phylipout phylipoutz7Output format: phylip (True), or fasta (False, default)z --inputorder inputorderzFOutput order: same as input (True, default) or alignment based (False)z --reorderreorderz?Output order: aligned (True) or in input order (False, default)z --treeouttreeoutzJGuide tree is output to the input.tree file (True) or not (False, default)z--quietquietz6Do not report progress (True) or not (False, default).z--nucnucz?Assume the sequences are nucleotide (True/False). Default: autoz--aminoaminoz?Assume the sequences are amino acid (True/False). Default: autoz--seedseedzXSeed alignments given in alignment_n (fasta format) are aligned with sequences in input.inputzInput file name)r= is_requiredinput1z4Second input file name for the mafft-profile command)r=N)rrr parametersr__init__)selfcmdkwargsrr9rrNUs %-5>FMTZahqy '/8@HPX` hpz #).4:?HPSYzMafftCommandline.__init__N)r)__name__ __module__ __qualname____doc__rNrrrrrsEr__main__) run_doctestN) rUBio.ApplicationrrrrrrR Bio._utilsrWrrrrs    &