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| #!/usr/bin/perl -w
use strict;
use warnings;
use Bio::SeqIO;
use vars qw(@ISA);
use Bio::Tools::Run::PiseApplication;
@ISA = qw(Bio::Tools::Run::PiseApplication);
sub new {
my ($class, $location, $email, @params) = @_;
my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/msbar.pm
$self->{COMMAND} = "msbar";
$self->{VERSION} = "5.a";
$self->{TITLE} = "MSBAR";
$self->{DESCRIPTION} = "Mutate sequence beyond all recognition (EMBOSS)";
$self->{OPT_EMAIL} = 0;
$self->{CATEGORIES} = [
"nucleic:mutation",
"protein:mutation",
];
$self->{DOCLINK} = "http://www.uk.embnet.org/Software/EMBOSS/Apps/msbar.html";
$self->{_INTERFACE_STANDOUT} = undef;
$self->{_STANDOUT_FILE} = undef;
$self->{TOP_PARAMETERS} = [
"msbar",
"init",
"input",
"required",
"advanced",
"output",
"auto",
];
$self->{PARAMETERS_ORDER} = [
"msbar",
"init",
"input", # input Section
"sequence", # sequence -- any [sequences] (-sequence)
"required", # required Section
"count", # Number of times to perform the mutation operations (-count)
"point", # Types of point mutations to perform -- Point mutation operations [select values] (-point)
"block", # Types of block mutations to perform -- Block mutation operations [select values] (-block)
"advanced", # advanced Section
"inframe", # Do 'codon' and 'block' operations in frame (-inframe)
"codon", # Types of codon mutations to perform -- Codon mutation operations [select values] (-codon)
"minimum", # Minimum size for a block mutation (-minimum)
"maximum", # Maximum size for a block mutation (-maximum)
"other", # Other sequences that the mutated result should not match (-other)
"output", # output Section
"outseq", # outseq (-outseq)
"outseq_sformat", # Output format for: outseq
"auto",
];
$self->{TYPE} = {
"msbar" => 'String',
"init" => 'String',
"input" => 'Paragraph',
"sequence" => 'Sequence',
"required" => 'Paragraph',
"count" => 'Integer',
"point" => 'List',
"block" => 'List',
"advanced" => 'Paragraph',
"inframe" => 'Switch',
"codon" => 'List',
"minimum" => 'Integer',
"maximum" => 'Integer',
"other" => 'Sequence',
"output" => 'Paragraph',
"outseq" => 'OutFile',
"outseq_sformat" => 'Excl',
"auto" => 'String',
};
$self->{FORMAT} = {
"init" => {
"perl" => ' "" ',
},
"input" => {
},
"sequence" => {
"perl" => '" -sequence=$value -sformat=fasta"',
},
"required" => {
},
"count" => {
"perl" => '" -count=$value"',
},
"point" => {
"perl" => '" -point=$value"',
},
"block" => {
"perl" => '" -block=$value"',
},
"advanced" => {
},
"inframe" => {
"perl" => '($value)? " -inframe" : ""',
},
"codon" => {
"perl" => '" -codon=$value"',
},
"minimum" => {
"perl" => '(defined $value && $value != $vdef)? " -minimum=$value" : ""',
},
"maximum" => {
"perl" => '(defined $value && $value != $vdef)? " -maximum=$value" : ""',
},
"other" => {
"perl" => '($value && $value ne $vdef)? " -other=$value -sformat=fasta" : ""',
},
"output" => {
},
"outseq" => {
"perl" => '" -outseq=$value"',
},
"outseq_sformat" => {
"perl" => '" -osformat=$value"',
},
"auto" => {
"perl" => '" -auto -stdout"',
},
"msbar" => {
"perl" => '"msbar"',
}
};
$self->{FILENAMES} = {
};
$self->{SEQFMT} = {
"sequence" => [8],
"other" => [8],
};
$self->{GROUP} = {
"init" => -10,
"sequence" => 1,
"count" => 2,
"point" => 3,
"block" => 4,
"inframe" => 5,
"codon" => 6,
"minimum" => 7,
"maximum" => 8,
"other" => 9,
"outseq" => 10,
"outseq_sformat" => 11,
"auto" => 12,
"msbar" => 0
};
$self->{BY_GROUP_PARAMETERS} = [
"init",
"input",
"required",
"advanced",
"output",
"msbar",
"sequence",
"count",
"point",
"block",
"inframe",
"codon",
"minimum",
"maximum",
"other",
"outseq",
"outseq_sformat",
"auto",
];
$self->{SIZE} = {
};
$self->{ISHIDDEN} = {
"init" => 1,
"input" => 0,
"sequence" => 0,
"required" => 0,
"count" => 0,
"point" => 0,
"block" => 0,
"advanced" => 0,
"inframe" => 0,
"codon" => 0,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 0,
"outseq_sformat" => 0,
"auto" => 1,
"msbar" => 1
};
$self->{ISCOMMAND} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"count" => 0,
"point" => 0,
"block" => 0,
"advanced" => 0,
"inframe" => 0,
"codon" => 0,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 0,
"outseq_sformat" => 0,
"auto" => 0,
};
$self->{ISMANDATORY} = {
"init" => 0,
"input" => 0,
"sequence" => 1,
"required" => 0,
"count" => 1,
"point" => 1,
"block" => 1,
"advanced" => 0,
"inframe" => 0,
"codon" => 1,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 1,
"outseq_sformat" => 0,
"auto" => 0,
};
$self->{PROMPT} = {
"init" => "",
"input" => "input Section",
"sequence" => "sequence -- any [sequences] (-sequence)",
"required" => "required Section",
"count" => "Number of times to perform the mutation operations (-count)",
"point" => "Types of point mutations to perform -- Point mutation operations [select values] (-point)",
"block" => "Types of block mutations to perform -- Block mutation operations [select values] (-block)",
"advanced" => "advanced Section",
"inframe" => "Do 'codon' and 'block' operations in frame (-inframe)",
"codon" => "Types of codon mutations to perform -- Codon mutation operations [select values] (-codon)",
"minimum" => "Minimum size for a block mutation (-minimum)",
"maximum" => "Maximum size for a block mutation (-maximum)",
"other" => "Other sequences that the mutated result should not match (-other)",
"output" => "output Section",
"outseq" => "outseq (-outseq)",
"outseq_sformat" => "Output format for: outseq",
"auto" => "",
};
$self->{ISSTANDOUT} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"count" => 0,
"point" => 0,
"block" => 0,
"advanced" => 0,
"inframe" => 0,
"codon" => 0,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 0,
"outseq_sformat" => 0,
"auto" => 0,
};
$self->{VLIST} = {
"input" => ['sequence',],
"required" => ['count','point','block',],
"point" => ['0','None','1','Any of the following','2','Insertions','3','Deletions','4','Changes','5','Duplications','6','Moves',],
"block" => ['0','None','1','Any of the following','2','Insertions','3','Deletions','4','Changes','5','Duplications','6','Moves',],
"advanced" => ['inframe','codon','minimum','maximum','other',],
"codon" => ['0','None','1','Any of the following','2','Insertions','3','Deletions','4','Changes','5','Duplications','6','Moves',],
"output" => ['outseq','outseq_sformat',],
"outseq_sformat" => ['fasta','fasta','gcg','gcg','phylip','phylip','embl','embl','swiss','swiss','ncbi','ncbi','nbrf','nbrf','genbank','genbank','ig','ig','codata','codata','strider','strider','acedb','acedb','staden','staden','text','text','fitch','fitch','msf','msf','clustal','clustal','phylip','phylip','phylip3','phylip3','asn1','asn1',],
};
$self->{FLIST} = {
};
$self->{SEPARATOR} = {
"point" => ",",
"block" => ",",
"codon" => ",",
};
$self->{VDEF} = {
"count" => '1',
"point" => ['0',],
"block" => ['0',],
"inframe" => '0',
"codon" => ['0',],
"minimum" => '1',
"maximum" => '10',
"outseq" => 'outseq.out',
"outseq_sformat" => 'fasta',
};
$self->{PRECOND} = {
"init" => { "perl" => '1' },
"input" => { "perl" => '1' },
"sequence" => { "perl" => '1' },
"required" => { "perl" => '1' },
"count" => { "perl" => '1' },
"point" => { "perl" => '1' },
"block" => { "perl" => '1' },
"advanced" => { "perl" => '1' },
"inframe" => { "perl" => '1' },
"codon" => {
"acd" => '@($(sequence.protein)?N:Y)',
},
"minimum" => { "perl" => '1' },
"maximum" => { "perl" => '1' },
"other" => { "perl" => '1' },
"output" => { "perl" => '1' },
"outseq" => { "perl" => '1' },
"outseq_sformat" => { "perl" => '1' },
"auto" => { "perl" => '1' },
};
$self->{CTRL} = {
};
$self->{PIPEOUT} = {
"outseq" => {
'1' => "seqsfile",
},
};
$self->{WITHPIPEOUT} = {
};
$self->{PIPEIN} = {
"sequence" => {
"seqsfile" => '1',
},
};
$self->{WITHPIPEIN} = {
};
$self->{ISCLEAN} = {
"init" => 0,
"input" => 0,
"sequence" => 0,
"required" => 0,
"count" => 0,
"point" => 0,
"block" => 0,
"advanced" => 0,
"inframe" => 0,
"codon" => 0,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 0,
"outseq_sformat" => 0,
"auto" => 0,
};
$self->{ISSIMPLE} = {
"init" => 0,
"input" => 0,
"sequence" => 1,
"required" => 0,
"count" => 1,
"point" => 1,
"block" => 1,
"advanced" => 0,
"inframe" => 0,
"codon" => 1,
"minimum" => 0,
"maximum" => 0,
"other" => 0,
"output" => 0,
"outseq" => 1,
"outseq_sformat" => 1,
"auto" => 0,
};
$self->{PARAMFILE} = {
};
$self->{COMMENT} = {
"codon" => [
"Types of codon mutations to perform. These are only done if the sequence is nucleic.",
],
"other" => [
"If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here. If you want the result to be different to previous results of this program, specify the previous result sequences here. The program will check that the result does not match the sequences specified here before writing it out. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message.",
],
};
$self->{SCALEMIN} = {
};
$self->{SCALEMAX} = {
};
$self->{SCALEINC} = {
};
$self->{INFO} = {
};
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/msbar.pm
$self->_init_params(@params);
return $self;
}
1; # Needed to keep compiler happy
} |
Bio: :Tools::Run::Pise Application: :msbar
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