# Copyright 2009 by Cymon J. Cox. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Command line wrapper for the multiple alignment program DIALIGN2-2.""" from Bio.Application import _Argument from Bio.Application import _Option from Bio.Application import _Switch from Bio.Application import AbstractCommandline class DialignCommandline(AbstractCommandline): """Command 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. """ def __init__(self, cmd="dialign2-2", **kwargs): """Initialize the class.""" self.program_name = cmd self.parameters = [ _Switch( ["-afc", "afc"], r"Creates additional output file '\*.afc' " "containing data of all fragments considered " "for alignment WARNING: this file can be HUGE !", ), _Switch( ["-afc_v", "afc_v"], "Like '-afc' but verbose: fragments are explicitly " "printed. WARNING: this file can be EVEN BIGGER !", ), _Switch( ["-anc", "anc"], "Anchored alignment. Requires a file .anc " "containing anchor points.", ), _Switch( ["-cs", "cs"], "If segments are translated, not only the 'Watson " "strand' but also the 'Crick strand' is looked at.", ), _Switch(["-cw", "cw"], "Additional output file in CLUSTAL W format."), _Switch( ["-ds", "ds"], "'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.", ), _Switch(["-fa", "fa"], "Additional output file in FASTA format."), _Switch( ["-ff", "ff"], r"Creates file \*.frg containing information about all " "fragments that are part of the respective optimal " "pairwise alignmnets plus information about " "consistency in the multiple alignment", ), _Option( ["-fn", "fn"], "Output files are named ..", equate=False, ), _Switch( ["-fop", "fop"], r"Creates file \*.fop containing coordinates of all " "fragments that are part of the respective pairwise alignments.", ), _Switch( ["-fsm", "fsm"], r"Creates file \*.fsm containing coordinates of all " "fragments that are part of the final alignment", ), _Switch( ["-iw", "iw"], "Overlap 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.", ), _Switch( ["-lgs", "lgs"], "'long genomic sequences' - combines the following " "options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, " "-fop, -ff, -cs, -ds, -pst ", ), _Switch( ["-lgs_t", "lgs_t"], "Like '-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.", ), _Option( ["-lmax", "lmax"], "Maximum fragment length = x (default: x = 40 or " "x = 120 for 'translated' fragments). Shorter x " "speeds up the program but may affect alignment quality.", checker_function=lambda x: isinstance(x, int), equate=False, ), _Switch( ["-lo", "lo"], r"(Long Output) Additional file \*.log with information " "about fragments selected for pairwise alignment and " "about consistency in multi-alignment procedure.", ), _Switch( ["-ma", "ma"], "'mixed alignments' consisting of P-fragments and " "N-fragments if nucleic acid sequences are aligned.", ), _Switch( ["-mask", "mask"], "Residues not belonging to selected fragments are " r"replaced by '\*' characters in output alignment " "(rather than being printed in lower-case characters)", ), _Switch( ["-mat", "mat"], r"Creates file \*mat with substitution counts derived " "from the fragments that have been selected for alignment.", ), _Switch( ["-mat_thr", "mat_thr"], "Like '-mat' but only fragments with weight score " "> t are considered", ), _Switch( ["-max_link", "max_link"], "'maximum linkage' clustering used to construct " "sequence tree (instead of UPGMA).", ), _Switch(["-min_link", "min_link"], "'minimum linkage' clustering used."), _Option(["-mot", "mot"], "'motif' option.", equate=False), _Switch(["-msf", "msf"], "Separate output file in MSF format."), _Switch( ["-n", "n"], "Input sequences are nucleic acid sequences. " "No translation of fragments.", ), _Switch( ["-nt", "nt"], "Input sequences are nucleic acid sequences and " "'nucleic acid segments' are translated to 'peptide " "segments'.", ), _Switch( ["-nta", "nta"], "'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.", ), _Switch( ["-o", "o"], "Fast version, resulting alignments may be slightly different.", ), _Switch( ["-ow", "ow"], "Overlap weights enforced (By default, overlap weights " "are used only if up to 35 sequences are aligned since " "calculating overlap weights is time consuming).", ), _Switch( ["-pst", "pst"], r"'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.", ), _Switch( ["-smin", "smin"], "Minimum 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.", ), _Option( ["-stars", "stars"], r"Maximum number of '\*' characters indicating degree " "of local similarity among sequences. By default, no " "stars are used but numbers between 0 and 9, instead.", checker_function=lambda x: x in range(10), equate=False, ), _Switch(["-stdo", "stdo"], "Results written to standard output."), _Switch( ["-ta", "ta"], "Standard textual alignment printed (overrides " "suppression of textual alignments in special " "options, e.g. -lgs)", ), _Option( ["-thr", "thr"], "Threshold T = x.", checker_function=lambda x: isinstance(x, int), equate=False, ), _Switch( ["-xfr", "xfr"], "'exclude fragments' - list of fragments can be " "specified that are NOT considered for pairwise alignment", ), _Argument( ["input"], "Input file name. Must be FASTA format", filename=True, is_required=True, ), ] AbstractCommandline.__init__(self, cmd, **kwargs) if __name__ == "__main__": from Bio._utils import run_doctest run_doctest()