o RŀgH)@sZdZddlmZddlmZddlmZGdddeZedkr+ddlmZed Sd S) z>Command line wrapper for the multiple alignment program PRANK.)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)PrankCommandlineaWCommand line wrapper for the multiple alignment program PRANK. http://www.ebi.ac.uk/goldman-srv/prank/prank/ Notes ----- Last checked against version: 081202 References ---------- Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557--10562. Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632. Examples -------- To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with "aligned" (you can't pick the filename explicitly), no tree output and no XML output, use: >>> from Bio.Align.Applications import PrankCommandline >>> prank_cline = PrankCommandline(d="unaligned.fasta", ... o="aligned", # prefix only! ... f=8, # FASTA output ... notree=True, noxml=True) >>> print(prank_cline) prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree You would typically run the command line with prank_cline() or via the Python subprocess module, as described in the Biopython tutorial. prankc sttddgtddgddddtdd gd dd td d gdtddgdtddgddd tddgdfdddtddgdtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,tgd-d.td/d0gd1td2d3gd4d5ddtd6d7gd8d9ddtd:d;gdd?gd@dAddtdBdCgdDdEddtdFdGgdHtdIdJgdKtdLdMgdNtdOdPgdQdRddtdSdTgdUtdVdWgdXtdYdZgd[td\d]gd^td_d`gdatdbdcgddtdedfgdgdhddtdidjgdkdlddtdmdngdotdpdqgdrtdsdtgdudvddtdwdxgdydzddtd{d|gd}d~ddtddgddddtddgdtddgdtddgdtddgd|_tj||fi|dS)zInitialize the class.z-ddzInput filenameT)filename is_requiredz-ttzInput guide tree filename)r z-treetreez!Input guide tree as Newick stringz-mmz8User-defined alignment model filename. Default: HKY2/WAGz-oozOutput filenames prefix. Default: 'output' Will write: output.?.fas (depending on requested format), output.?.xml and output.?.dndz-ffzOutput alignment format. Default: 8 FASTA Option are: 1. IG/Stanford 8. Pearson/Fasta 2. GenBank/GB 11. Phylip3.2 3. NBRF 12. Phylip 4. EMBL 14. PIR/CODATA 6. DNAStrider 15. MSF 7. Fitch 17. PAUP/NEXUScs|vSNxOUTPUT_FORMAT_VALUESrQ/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_Prank.pyWsz+PrankCommandline.__init__..)checker_functionz-noxmlnoxmlz>Do not output XML files (PRANK versions earlier than v.120626)z-notreenotreezCDo not output dnd tree files (PRANK versions earlier than v.120626)z-showxmlshowxmlz+Output XML files (PRANK v.120626 and later)z -showtreeshowtreez0Output dnd tree files (PRANK v.120626 and later)z -shortnames shortnameszTruncate names at first spacez-quietquietzReduce verbosity)z-Fz+FFz1Force insertions to be always skipped: same as +Fz-dotsdotszShow insertion gaps as dotsz-gaprategapratez0Gap opening rate. Default: dna 0.025 prot 0.0025cS t|tSr isinstancefloatrrrrrv z-gapextgapextz6Gap extension probability. Default: dna 0.5 / prot 0.5cSr#rr$rrrrr|r'z -dnafreqsdnafreqszdDNA frequencies - 'A,C,G,T'. eg '25,25,25,25' as a quote surrounded string value. Default: empiricalcSr#r)r%bytesrrrrrr'z-kappakappaz)Transition/transversion ratio. Default: 2cSr#rr%intrrrrrr'z-rhorhoz#Purine/pyrimidine ratio. Default: 1cSr#rr,rrrrrr'z-codoncodonzCodon aware alignment or notz-termgaptermgapzPenalise terminal gaps normallyz-nopostnopostz2Do not compute posterior support. Default: computez-pwdistpwdistzPExpected pairwise distance for computing guidetree. Default: dna 0.25 / prot 0.5cSr#rr$rrrrrr'z-onceoncez3Run only once. Default: twice if no guidetree givenz-twicetwicezAlways run twicez-skipinsskipinsz$Skip insertions in posterior supportz-uselogsuselogsz8Slower but should work for a greater number of sequencesz -writeancwriteanczOutput ancestral sequencesz -printnodes printnodesz&Output each node; mostly for debuggingz -matresize matresizezMatrix resizing multipliercSt|ttfSrr%r&r-rrrrrz -matinitsize matinitsizezMatrix initial size multipliercSr:rr;rrrrrr<z-longseqlongseqz!Save space in pairwise alignmentsz -pwgenomic pwgenomicz#Do pairwise alignment, no guidetreez-pwgenomicdist pwgenomicdistz-Distance for pairwise alignment. Default: 0.3cSr#rr$rrrrrr'z-scalebranches scalebranchesz-Scale branch lengths. Default: dna 1 / prot 2cSr#rr,rrrrrr'z-fixedbranches fixedbranchesz'Use fixed branch lengths of input valuecSr#rr$rrrrrr'z -maxbranches maxbranchesz)Use maximum branch lengths of input valuecSr#rr$rrrrrr'z -realbranches realbranchesz Disable branch length truncationz -translate translatezTranslate to proteinz -mttranslate mttranslatez#Translate to protein using mt tablez-convertconvertz?Convert input alignment to new format. Do not perform alignmentN)listrangerr parametersr__init__)selfcmdkwargsrrrrK5s    !%), 0 15 9;AGNT Z \_ek n op tuz   $ '(,1zPrankCommandline.__init__N)r)__name__ __module__ __qualname____doc__rKrrrrrs&r__main__) run_doctestN) rRBio.ApplicationrrrrrO Bio._utilsrTrrrrs   ^