o Rŀg'@sfdZddlmZddlmZddlmZddlmZGdddeZedkr1dd lm Z e d Sd S) zCCommand line wrapper for the multiple alignment program DIALIGN2-2.) _Argument)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)DialignCommandlineaCommand line wrapper for the multiple alignment program DIALIGN2-2. http://bibiserv.techfak.uni-bielefeld.de/dialign/welcome.html Notes ----- Last checked against version: 2.2 References ---------- B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ. Nucleic Acids Research 32, W33-W36. Examples -------- To align a FASTA file (unaligned.fasta) with the output files names aligned.* including a FASTA output file (aligned.fa), use: >>> from Bio.Align.Applications import DialignCommandline >>> dialign_cline = DialignCommandline(input="unaligned.fasta", ... fn="aligned", fa=True) >>> print(dialign_cline) dialign2-2 -fa -fn aligned unaligned.fasta You would typically run the command line with dialign_cline() or via the Python subprocess module, as described in the Biopython tutorial. dialign2-2cKsT||_gtddgdtddgdtddgd td d gd td dgdtddgdtddgdtddgdtddgdddtddgd td!d"gd#td$d%gd&td'd(gd)td*d+gd,td-d.gd/d0d1dd2td3d4gd5td6d7gd8td9d:gd;tdtd?d@gdAtdBdCgdDtdEdFgdGtdHdIgdJddtdKdLgdMtdNdOgdPtdQdRgdStdTdUgdVtdWdXgdYtdZd[gd\td]d^gd_td`dagdbtdcddgdedfd1dd2tdgdhgditdjdkgdltdmdngdodpd1dd2tdqdrgdstdtgdudvdvdw|_tj||fi|dxS)yzInitialize the class.z-afcafczCreates additional output file '\*.afc' containing data of all fragments considered for alignment WARNING: this file can be HUGE !z-afc_vafc_vzbLike '-afc' but verbose: fragments are explicitly printed. WARNING: this file can be EVEN BIGGER !z-ancanczLAnchored alignment. Requires a file .anc containing anchor points.z-cscszbIf segments are translated, not only the 'Watson strand' but also the 'Crick strand' is looked at.z-cwcwz+Additional output file in CLUSTAL W format.z-dsdsz'dna alignment speed up' - non-translated nucleic acid fragments are taken into account only if they start with at least two matches. Speeds up DNA alignment at the expense of sensitivity.z-fafaz'Additional output file in FASTA format.z-ffffzCreates file \*.frg containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignmentz-fnfnz.Output files are named ..F)equatez-fopfopzpCreates file \*.fop containing coordinates of all fragments that are part of the respective pairwise alignments.z-fsmfsmz`Creates file \*.fsm containing coordinates of all fragments that are part of the final alignmentz-iwiwzOverlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned). This option speeds up the alignment but may lead to reduced alignment quality.z-lgslgsz'long genomic sequences' - combines the following options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst z-lgs_tlgs_tzLike '-lgs' but with all segment pairs assessed at the peptide level (rather than 'mixed alignments' as with the '-lgs' option). Therefore faster than -lgs but not very sensitive for non-coding regions.z-lmaxlmaxzMaximum fragment length = x (default: x = 40 or x = 120 for 'translated' fragments). Shorter x speeds up the program but may affect alignment quality.cS t|tSN isinstanceintxrS/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_Dialign.py~ z-DialignCommandline.__init__..)checker_functionrz-loloz(Long Output) Additional file \*.log with information about fragments selected for pairwise alignment and about consistency in multi-alignment procedure.z-mamazc'mixed alignments' consisting of P-fragments and N-fragments if nucleic acid sequences are aligned.z-maskmaskzResidues not belonging to selected fragments are replaced by '\*' characters in output alignment (rather than being printed in lower-case characters)z-matmatzmCreates file \*mat with substitution counts derived from the fragments that have been selected for alignment.z-mat_thrmat_thrzCLike '-mat' but only fragments with weight score > t are consideredz -max_linkmax_linkzP'maximum linkage' clustering used to construct sequence tree (instead of UPGMA).z -min_linkmin_linkz"'minimum linkage' clustering used.z-motmotz'motif' option.z-msfmsfz#Separate output file in MSF format.z-nnzHInput sequences are nucleic acid sequences. No translation of fragments.z-ntntzlInput sequences are nucleic acid sequences and 'nucleic acid segments' are translated to 'peptide segments'.z-ntantaz'no textual alignment' - textual alignment suppressed. This option makes sense if other output files are of interest -- e.g. the fragment files created with -ff, -fop, -fsm or -lo.z-ooz=Fast version, resulting alignments may be slightly different.z-owowzOverlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming).z-pstpstz'print status'. Creates and updates a file \*.sta with information about the current status of the program run. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time.z-sminsminzMinimum similarity value for first residue pair (or codon pair) in fragments. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity.z-starsstarszMaximum number of '\*' characters indicating degree of local similarity among sequences. By default, no stars are used but numbers between 0 and 9, instead.cSs |tdvS)N )rangerrrr r!s z-stdostdoz#Results written to standard output.z-tataznStandard textual alignment printed (overrides suppression of textual alignments in special options, e.g. -lgs)z-thrthrzThreshold T = x.cSrrrrrrr r!r"z-xfrxfrzg'exclude fragments' - list of fragments can be specified that are NOT considered for pairwise alignmentinputz%Input file name. Must be FASTA formatT)filename is_requiredN) program_namerrr parametersr__init__)selfcmdkwargsrrr r@-s   &+05<BIQW\bgl qr sty   ()/5:AzDialignCommandline.__init__N)r)__name__ __module__ __qualname____doc__r@rrrr rsr__main__) run_doctestN) rGBio.ApplicationrrrrrrD Bio._utilsrIrrrr s    e