#!/usr/bin/env perl ########################################################################### # # Copyright (C) 1997-2015 Nigel P. Brown # # (i) License # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # # (ii) Contacts # # Project Admin: Nigel P. Brown # Email: biomview@gmail.com # Project URL: http://bio-mview.sourceforge.net # # (iii) Citation # # Please acknowledge use of this Program by citing the following reference in # any published work including web-sites: # # Brown, N.P., Leroy C., Sander C. (1998) MView: A Web compatible database # search or multiple alignment viewer. Bioinformatics. 14(4):380-381. # # and provide a link to the MView project URL given above under 'Contacts'. # ########################################################################### # $Id: mview,v 1.79 2015/06/18 20:26:00 npb Exp $ my $VERSION = '1.59'; my $PATCH = ''; my $PROJECT = 'MView'; my $AUTHOR = "Nigel P. Brown"; my $VERSION = $VERSION . ($PATCH?".$PATCH":""); my $COPYYRS = "1997-2015"; my $PROJPTH = 'http://bio-mview.sourceforge.net'; my $AUTHMAIL = 'biomview@gmail.com'; ########################################################################### require 5.004; $^W=1; BEGIN {$::COMPILE_ERROR=0} #catch compile time method call failure use lib '/opt/chipster/tools/mview/lib'; use Getopt; use Bio::MView::Manager; use strict; exit 1 if $::COMPILE_ERROR; ########################################################################### my $PROG = Universal::basename($0); my $INVOKE = "$PROG @ARGV"; my $DOCTYPE = ''; my $SCRATCH = Universal::tmpfile("mview_$$"); my %KNOWN_FORMAT = ( #search formats 'blast' => 1, 'uvfasta' => 1, #flatfile formats 'plain' => 1, 'clustal' => 1, 'msf' => 1, 'fasta' => 1, 'pir' => 1, 'hssp' => 1, 'maf' => 1, 'multas' => 1, 'mips' => 1, 'jnetz' => 1, ); my ($HTML_NULL, $HTML_DATA, $HTML_CSS, $HTML_BODY, $HTML_HTML, $HTML_MIME) = (0,1,2,4,8,16); my ($VERB_NULL, $VERB_FILE, $VERB_ARGV, $VERB_FORM, $VERB_OPTS) = (0,1,2,4,8); my ($stm, $com, $opt, $par) = (\*STDOUT); ########################################################################### $SIG{'INT'} = sub { warn "$PROG: exiting on interrupt\n"; &cleanup(); exit 1 }; $com = new Getopt($PROG, \*DATA)->getoptions(\@ARGV); $opt = $com->get_option_hash; $par = $com->get_parameter_hash; rationalise_parameters($opt, $par); dump_options($opt, $par) if $opt->{'verbose'} & $VERB_OPTS; usage($com, $opt, $par, 0) if $opt->{'help'}; html_head($opt, $par, $stm); #echo command line? if ($opt->{'verbose'} & $VERB_ARGV) { my $s = $com->argv_string; $s =~ s/\-+v[a-z]*[=\s]+\S+\s*//g; if ($opt->{'html'}) { print $stm "

command line:

";
	print $stm "$PROG $s";
	print $stm "

produced:

\n"; } else { print $stm "command line:\n"; print $stm "$PROG $s\n"; print $stm "produced:\n\n"; } } #leading copyright? print $stm copyright($opt) if $opt->{'out'} eq 'rdb'; #colormap listing request: no alignment if ($opt->{'listcolors'}) { print $stm "

\n"       if $opt->{'html'};
    print $stm Bio::MView::Manager::list_colormaps($opt->{'html'});
    print $stm "

\n" if $opt->{'html'}; print $stm copyright($opt); html_foot($opt, $par, $stm); exit 0; } #groupmap listing request: no alignment if ($opt->{'listgroups'}) { print $stm "

\n"       if $opt->{'html'};
    print $stm Bio::MView::Manager::list_groupmaps($opt->{'html'});
    print $stm "

\n" if $opt->{'html'}; print $stm copyright($opt); html_foot($opt, $par, $stm); exit 0; } #CSS listing request: no alignment if ($opt->{'listcss'}) { #http://www.w3.org/TR/REC-CSS1#containment-in-html print $stm Bio::MView::Manager::list_css( 'alncolor' => $par->{'alncolor'}, 'labcolor' => $par->{'labcolor'}, 'symcolor' => $par->{'symcolor'}, 'gapcolor' => $par->{'gapcolor'}, ); exit 0; } #read from stdin? unless (@ARGV or $opt->{'noparse'}) { warn "$PROG: reading from standard input (Ctrl-C to cancel)\n"; open(TMP, ">$SCRATCH") or die "$PROG: nothing on stdin - exiting!\n"; while (<>) { print TMP } close TMP; push @ARGV, $SCRATCH; } #do the real work if (mview($opt, $par, $stm, @ARGV)) { print $stm copyright($opt) if $opt->{'html'} != $HTML_DATA and $opt->{'out'} =~ /^new/; } else { my $s = "$PROG: no alignments found\n"; print $s if $opt->{'html'} and $opt->{'html'} != $HTML_DATA; warn $s; } html_foot($opt, $par, $stm); #Universal::vmstat("FINISHED."); cleanup(); ########################################################################### sub mview { my ($opt, $par, $stm) = (shift, shift, shift); my ($mgr, $file, $format); #Universal::vmstat("Manager constructor"); $mgr = new Bio::MView::Manager($PROG, %$par); foreach $file (@_) { unless (-e $file) { warn "$PROG: '$file' does not exist\n"; next; } unless (-f $file) { warn "$PROG: '$file' is not a file\n"; next; } unless (-r $file) { warn "$PROG: '$file' is not readable\n"; next; } warn "$PROG: processing '$file'\n" if $opt->{'verbose'} & $VERB_FILE; #try to choose a format if one wasn't specified $format = (defined $opt->{'in'} ? $opt->{'in'} : check_format($file, 'file')); warn "$PROG: format is probably '$format'\n" if !defined $opt->{'in'} and $opt->{'verbose'} & $VERB_FORM; print $stm "

\n"    if $opt->{'pre'};

	if (! defined $mgr->parse($file, $format)) {
	    warn "$PROG: can't parse file '$file'\n";
	}

	print $stm "

\n" if $opt->{'pre'}; } #Universal::vmstat("Manager constructor done"); #colormap/groupmap listing request: no alignment return 0 if $par->{'noparse'}; #save printing until end? if ($par->{'register'} and $opt->{'out'} eq 'new') { $mgr->print; #Universal::vmstat("print done (mview)"); } return $mgr->alignment_count; } sub cleanup { unlink "$SCRATCH" if -f "$SCRATCH" } sub rationalise_parameters { my ($o, $p) = @_; #ignore HTML if RDB output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'rdb'; #ignore HTML if CLUSTAL output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'clustal'; #ignore HTML if PIR output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'pir'; #ignore HTML if MSF output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'msf'; #ignore HTML if fasta/pearson output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'fasta'; #ignore HTML if plain output ($o->{'html'}, $p->{'html'}) = (0, 0) if $p->{'mode'} eq 'plain'; #switch off preformatted flag if HTML is off $o->{'pre'} = 0 unless $o->{'html'}; #ignore style sheets if HTML off ($o->{'css'}, $p->{'css1'}) = ('off', 0) if $o->{'html'} == 0; #ignore style sheets in HTML if css is unset $o->{'html'} &= ($HTML_MIME|$HTML_HTML|$HTML_BODY|$HTML_DATA) if $o->{'css'} eq 'off'; #ignore coloring if HTML is off! unless ($o->{'html'}) { $p->{'aln_coloring'} = 'none'; $p->{'con_coloring'} = 'none'; } #switch off parsing if color/groupmap listing requested if ($o->{'listcolors'} or $o->{'listgroups'}) { $o->{'noparse'} = $p->{'noparse'} = 1; $o->{'pre'} = 0; } else { $o->{'noparse'} = $p->{'noparse'} = 0; } } sub html_head { my ($o, $p, $stm) = (@_, *STDOUT); #warn "HTML=$o->{'html'}\n"; return unless $o->{'html'}; return if $o->{'html'} == $HTML_DATA; #want MIME type? if ($o->{'html'} & $HTML_MIME) { print $stm "Content-Type: text/html\n\n"; } #want HTML HEAD? if ($o->{'html'} & $HTML_HTML) { print $stm "$DOCTYPE\n\n\n"; #want STYLE? if ($o->{'html'} & $HTML_CSS) { #link styles print $stm "\n"; #alignment styles if ($o->{'css'} =~ /^(?:file|http):/i) { #link to style sheet print $stm "{'css'}\">\n"; } else { #style sheet in situ print $stm "\n"; } } #want TITLE? (in titlebar) if (defined $o->{'title'}) { print $stm "$o->{'title'}\n"; } print $stm "\n"; } #want BODY? if ($o->{'html'} & $HTML_BODY) { print $stm "\n"; } #want TITLE? (in document) if (defined $o->{'title'}) { print $stm "

$o->{'title'}

\n"; } } sub html_foot { my ($o, $p, $stm) = (@_, *STDOUT); return unless $o->{'html'}; return if $o->{'html'} == $HTML_DATA; print $stm "\n" if $o->{'html'} & $HTML_BODY; print $stm "\n" if $o->{'html'} & $HTML_HTML; } sub check_format { sub FASTA { return 'Pearson' unless $_[1] eq 'file'; local $_, *TMP; my $guess = 'Pearson'; open(TMP, "< $_[0]") or die "$PROG: can't open '$_[0]'\n"; while () { next if /^\s*$/; $guess = 'FASTA' unless /^\s*>/; last; } close TMP; return $guess; } return map { lc $_ } sort keys %KNOWN_FORMAT unless @_; my ($base, $ext) = ($_[0], ''); ($base, $ext) = Universal::fileparts($_[0]) if $_[1] eq 'file'; #warn "($base, $ext)"; foreach ($ext) { #final extension starts with: return 'CLUSTAL' if $_ =~ /^aln/i; return 'CLUSTAL' if $_ =~ /^clu/i; return 'HSSP' if $_ =~ /^hss/i; return 'JNETZ' if $_ =~ /^jnt/i; return 'JNETZ' if $_ =~ /^jne/i; return 'MAF' if $_ =~ /^maf/i; return 'MIPS' if $_ =~ /^mip/i; return 'MSF' if $_ =~ /^msf/i; return 'MULTAS' if $_ =~ /^mul/i; return 'PIR' if $_ =~ /^pir/i; return 'Plain' if $_ =~ /^txt/i; return 'Plain' if $_ =~ /^pla/i; return 'Plain' if $_ =~ /^pln/i; return 'BLAST' if $_ =~ /^bla/i; return 'BLAST' if $_ =~ /^tbl/i; return 'BLAST' if $_ =~ /^phi/i; return 'BLAST' if $_ =~ /^psi/i; return 'FASTA' if $_ =~ /^tfa/i; return 'FASTA' if $_ =~ /^ggs/i; return 'FASTA' if $_ =~ /^gls/i; return 'FASTA' if $_ =~ /^ss/i; return FASTA(@_) if $_ =~ /^fa/i; } foreach ($base) { #basename contains: return 'CLUSTAL' if $_ =~ /aln/i; return 'CLUSTAL' if $_ =~ /clu/i; return 'HSSP' if $_ =~ /hssp/i; return 'JNETZ' if $_ =~ /jnet/i; return 'MAF' if $_ =~ /maf/i; return 'MIPS' if $_ =~ /mips/i; return 'MSF' if $_ =~ /msf/i; return 'MULTAS' if $_ =~ /multal/i; return 'MULTAS' if $_ =~ /multas/i; return 'PIR' if $_ =~ /pir/i; return 'Plain' if $_ =~ /plain/i; return 'BLAST' if $_ =~ /blast/i; return 'BLAST' if $_ =~ /tblast/i; return 'BLAST' if $_ =~ /phi.*blast/i; return 'BLAST' if $_ =~ /psi.*blast/i; return 'FASTA' if $_ =~ /ggsearch/i; return 'FASTA' if $_ =~ /glsearch/i; return 'FASTA' if $_ =~ /ssearch/i; return 'FASTA' if $_ =~ /uvf/i; return 'FASTA' if $_ =~ /tfast/i; return 'FASTA' if $_ =~ /fast[fmsxy]/i; return FASTA(@_) if $_ =~ /fasta/i; return 'Pearson' if $_ =~ /pear/i; } #unknown format warn "$PROG: can't determine format of '$_[0]'\n"; cleanup(); exit 1; } sub usage { my ($com, $opt, $par, $exit, $stm) = (@_, *STDOUT); $opt->{'title'} = 'MView command line options'; html_head($opt, $par, $stm); print $stm "

\n"       if $opt->{'html'};
    $com->usage($stm);
    print $stm "

\n" if $opt->{'html'}; print $stm copyright($opt); html_foot($opt, $par, $stm); exit $exit if defined $exit; } sub dump_options { my ($opt, $par) = @_; warn "Input options:\n"; map { warn sprintf("%-25s => %s\n", $_, (defined $opt->{$_}?$opt->{$_}:'undef')) } sort keys %$opt; warn "\nPassed parameters:\n"; map { warn sprintf("%-25s => %s\n", $_, (defined $par->{$_}?$par->{$_}:'undef')) } sort keys %$par; warn "\n"; } sub copyright { my ($opt) = @_; my $s = ''; no strict; if ($opt->{'out'} eq 'rdb') { #rdb files $s .= "# $PROJECT $VERSION, Copyright (C) $COPYYRS $AUTHOR\n"; $s .= "# $INVOKE\n"; return $s; } if ($opt->{'html'}) { #any HTML $s .= "

$PROJECT "; $s .= "$VERSION, Copyright \© "; $s .= "$COPYYRS $AUTHOR"; $s .= "
\n"; return $s; } if ($opt->{'noparse'}) { #listcolor/listgroups without HTML $s .= "# $PROJECT $VERSION, Copyright (C) $COPYYRS $AUTHOR\n"; return $s; } $s = "\n$PROJECT $VERSION, Copyright (C) $COPYYRS $AUTHOR\n\n"; $s; } ########################################################################### __DATA__ text: "usage: __PROG [options] [file...]\n\n Option names and parameter values can generally be abbreviated. Alternative\n parameter values are listed in braces {}, followed by the default value in\n square brackets [].\n\n Some options take multiple arguments which must be supplied as a comma\n separated list, like '1,8,9,10'. Subranges are allowed, so you could also\n write that as '1,8:10' or even '1,8..10'. Any argument must be quoted if it\n contains whitespace or a wildcard that might be expanded by the shell\n" ########################################################################### #silent options because no 'usage:' field. [SILENT] #force @ARGV to be examined for '-help' first. OPTION: help default: 0 action: sub { __ARGS; __OPTION{__ON} = 1 if __OV } #force @ARGV to be examined for '-listcolors' first. OPTION: listcolors default: 0 action: sub { __ARGS; __OPTION{__ON} = 1 if __OV } #force @ARGV to be examined for '-listgroups' first. OPTION: listgroups default: 0 action: sub { __ARGS; __OPTION{__ON} = 1 if __OV } #force @ARGV to be examined for '-listcss' first. OPTION: listcss default: 0 action: sub { __ARGS; __OPTION{__ON} = 1 if __OV } #force @ARGV to be examined for '-colorfile' first. OPTION: colorfile type: s action: sub { __ARGS; local *TMP; if (defined __OV) { open(TMP, "< __OV") or CORE::die "__PROG: can't open colormap file '__OV'\n"; Bio::MView::Manager::load_colormaps(\*TMP); close TMP; } } #force @ARGV to be examined for '-groupfile' first. OPTION: groupfile type: s action: sub { __ARGS; local *TMP; if (defined __OV) { open(TMP, "< __OV") or CORE::die "__PROG: can't open consensus group file '__OV'\n"; Bio::MView::Manager::load_groupmaps(\*TMP); close TMP; } } #set the default colormaps and groupmaps (assume protein) OPTION: aa action: sub { __ARGS; (__PARAM{'def_aln_colormap'}, __PARAM{'def_con_colormap'}) = Bio::MView::Manager::get_default_colormaps('aa'); __PARAM{'def_aln_groupmap'} = __PARAM{'def_con_groupmap'} = Bio::MView::Manager::get_default_groupmap('aa'); __PARAM{'moltype'} = 'aa'; return 0; } #verbosity level, normally 0 to keep quiet OPTION: verbose type: i default: 0 #obsolete options: report fact to user OPTION: dna action: sub { __ARGS; __WARN("obsolete option '-__ON' replaced by '-moltype dna'") if defined __OV; } OPTION: keep action: sub { __ARGS; __WARN("obsolete option '-__ON' renamed as '-show'") if defined __OV; } OPTION: disc action: sub { __ARGS; __WARN("obsolete option '-__ON' renamed as '-hide'") if defined __OV; } ########################################################################### [FORMATS] text: "Input/output formats:" OPTION: in usage: "Input __CHOOSE(main::check_format)" type: s action: sub { __ARGS; return __OPTION{__ON} = main::check_format(__OV, 'par') if defined __OV; return; } OPTION: out usage: "Output __CHOOSE(Bio::MView::Manager::check_convert_mode)" type: s default: new param: mode convert: sub { __ARGS; __OPTION{'pre'} = 1; if (__OV =~ /^n/i) { #default __PV = 'new'; __OPTION{'pre'} = 0; } elsif (__OV =~ /^pl/i) { #plain __PV = 'plain'; } elsif (__OV =~ /^fa/i) { #Pearson/FASTA __PV = 'pearson'; } elsif (__OV =~ /^pe/i) { #Pearson/FASTA __PV = 'pearson'; } elsif (__OV =~ /^pi/i) { #PIR __PV = 'pir'; } elsif (__OV =~ /^ms/i) { #MSF __PV = 'msf'; } elsif (__OV =~ /^cl/i) { #CLUSTAL/aln __PV = 'clustal'; } elsif (__OV =~ /^al/i) { #CLUSTAL/aln __PV = 'clustal'; } elsif (__OV =~ /^rd/i) { #RDB __PV = 'rdb'; __OPTION{'pre'} = 0; } else { __WARN("unknown output format '-__ON=__OV'."); } __PV; } ########################################################################### [CONTENT] text: "Main formatting options:" OPTION: ruler usage: "Show ruler" type: b default: off param: OPTION: alignment usage: "Show alignment" type: b default: on param: OPTION: conservation usage: "Show clustal conservation line" type: b default: off param: OPTION: consensus usage: "Show consensus" type: b default: off param: OPTION: width usage: "Paginate alignment in blocks of N columns {N,flat}" type: s default: flat param: convert: sub { __ARGS; if (__OV eq 'flat') { return 0; } else { return __TEST('i', __ON, __OV); } } ########################################################################### [IDENTITY] text: "Percent identity calculations" OPTION: pcid usage: "Compute percent identities with respect to __CHOOSE(Bio::MView::Manager::check_identity_mode)" type: s default: 'aligned' param: convert: sub { __ARGS; return 'reference' if __OV =~ /^r/; return 'aligned' if __OV =~ /^a/; return 'hit' if __OV =~ /^h/; __WARN("bad setting '-__ON=__OV'."); __WARN("known percent identity methods are: ", join(",", Bio::MView::Manager::check_identity_mode), "\n"); } OPTION: reference usage: "Use row N or row identifier as %identity reference" type: s default: query param: ref_id ########################################################################### [FILTER] text: "General row/column filters:" OPTION: top usage: "Report top N hits" type: s default: all param: topn convert: sub { __ARGS; return 0 if __OV eq 'all'; return __TEST('i', __ON, __OV); } OPTION: maxident usage: "Only report sequences with percent identity <= N" type: f default: 100 param: convert: sub { __ARGS; if (__OV < 0 or __OV > 100) { __WARN("bad setting '-__ON=__OV', want range 0..100."); } __OV; } OPTION: minident usage: "Only report sequences with percent identity >= N" type: f default: 0 param: convert: sub { __ARGS; if (__OV < 0 or __OV > 100) { __WARN("bad setting '-__ON=__OV', want range 0..100."); } __OV; } OPTION: show usage: "Keep rows 1..N or identifiers" type: @s param: keeplist OPTION: hide usage: "Hide rows 1..N or identifiers" type: @s param: skiplist OPTION: nops usage: "No operation: exclude rows 1..N or identifiers from calculatons" type: @s param: nopslist OPTION: range usage: "Display column range M:N as numbered by ruler" type: s default: all param: convert: sub { __ARGS; my @tmp = (); if (__OV ne 'all') { @tmp = split(/:/, __OV); if (@tmp != 2) { __WARN("bad range setting '-__ON=__OV', want M:N."); } else { __TEST('i', __ON, $tmp[0]); __TEST('i', __ON, $tmp[1]); #ignore range order, but check for negative values if ($tmp[0] < 1 or $tmp[1] < 1) { __WARN("bad range setting '-__ON=__OV', want M:N."); } } } return [ @tmp ]; } ########################################################################### [MOLTYPE] text: "Molecule type:" OPTION: moltype usage: "Affects coloring and format converions __CHOOSE(Bio::MView::Manager::check_molecule_type)" type: s default: aa param: moltype convert: sub { __ARGS; if (__OV =~ /^aa/i) { __PV = 'aa'; } elsif (__OV =~ /^na/i) { __PV = 'na'; } elsif (__OV =~ /^dna/i) { __PV = 'dna'; } elsif (__OV =~ /^rna/i) { __PV = 'rna'; } unless (defined __PV and defined Bio::MView::Manager::check_molecule_type(__PV)) { __WARN("unknown molecule type '-__ON=__OV'."); __WARN("known types are: ", join(",", Bio::MView::Manager::check_molecule_type), "\n"); } (__PARAM{'def_aln_colormap'}, __PARAM{'def_con_colormap'}) = Bio::MView::Manager::get_default_colormaps(__PV); __PARAM{'def_aln_groupmap'} = __PARAM{'def_con_groupmap'} = Bio::MView::Manager::get_default_groupmap(__OV); __PARAM{'moltype'} = __PV; __PV; } ########################################################################### [ALN] text: "Alignment coloring:" OPTION: coloring usage: "Basic style of coloring __CHOOSE(Bio::MView::Manager::check_alignment_color_scheme)" type: s default: none param: aln_coloring convert: sub { __ARGS; if (__OV =~ /^n/i) { __PV = 'none'; } elsif (__OV =~ /^a/i) { __PV = 'any'; } elsif (__OV =~ /^i/i) { __PV = 'identity'; } elsif (__OV =~ /^c/i) { __PV = 'consensus'; } elsif (__OV =~ /^g/i) { __PV = 'group'; } unless (defined __PV and defined Bio::MView::Manager::check_alignment_color_scheme(__PV)) { __WARN("unknown coloring scheme '-__ON=__OV'."); __WARN("known color schemes are: ", join(",", Bio::MView::Manager::check_alignment_color_scheme), "\n"); } __PV; } OPTION: colormap usage: "Name of colormap to use" type: s param: aln_colormap convert: sub { __ARGS; if (defined __OV) { __PV = __OV; } else { __PV = __PARAM{'def_aln_colormap'}; } __PV = Bio::MView::Manager::check_colormap(__PV); unless (defined __PV) { __WARN("unknown colormap '-__ON=__OV'."); __WARN("known maps are: ", join(",", Bio::MView::Manager::check_colormap), "\n"); } __DELETE_PARAM('def_aln_colormap'); __PV; } OPTION: groupmap usage: "Name of groupmap to use if coloring by consensus" type: s param: aln_groupmap convert: sub { __ARGS; if (defined __OV) { __PV = __OV; } else { __PV = __PARAM{'def_aln_groupmap'}; } __PV = Bio::MView::Manager::check_groupmap(__PV); unless (defined __PV) { __WARN("unknown groupmap '-__ON=__OV'."); __WARN("known maps are: ", join(",", Bio::MView::Manager::check_groupmap), "\n"); } __DELETE_PARAM('def_aln_groupmap'); __PV; } OPTION: threshold usage: "Threshold percentage for consensus coloring" type: f default: 70 param: aln_threshold convert: sub { __ARGS; if (__OV < 50 or __OV > 100) { __WARN("bad value for '-__ON=__OV' must be in range 50..100."); } [ __OV ]; } OPTION: ignore usage: "Ignore singleton or class groups __CHOOSE(Bio::MView::Manager::check_ignore_class)" type: s default: none param: aln_ignore convert: sub { __ARGS; __PV = Bio::MView::Manager::check_ignore_class(__OV); if (!defined __PV) { __WARN("unknown alignment ignore mode '-__ON=__OV'."); __WARN("known ignore classes are: ", join(",", Bio::MView::Manager::check_ignore_class), "\n"); } __PV; } ########################################################################### [CON] text: "Consensus coloring:" OPTION: con_coloring usage: "Basic style of coloring __CHOOSE(Bio::MView::Manager::check_consensus_color_scheme)" type: s default: none param: con_coloring convert: sub { __ARGS; if (__OV =~ /^n/i) { __PV = 'none'; } elsif (__OV =~ /^a/i) { __PV = 'any'; } elsif (__OV =~ /^i/i) { __PV = 'identity'; } elsif (__OV =~ /^c/i) { __PV = 'consensus'; } elsif (__OV =~ /^g/i) { __PV = 'group'; } unless (defined __PV and defined Bio::MView::Manager::check_consensus_color_scheme(__PV)) { __WARN("unknown coloring scheme '-__ON=__OV'."); __WARN("known color schemes are: ", join(",", Bio::MView::Manager::check_consensus_color_scheme), "\n"); } __PV; } OPTION: con_colormap usage: "Name of colormap to use" type: s param: con_colormap convert: sub { __ARGS; if (defined __OV) { __PV = __OV; } else { __PV = __PARAM{'def_con_colormap'}; } __PV = __PARAM{'def_con_colormap'} unless defined __OV; __PV = Bio::MView::Manager::check_colormap(__PV); unless (defined __PV) { __WARN("unknown colormap '-__ON=__OV'."); __WARN("known maps are: ", join(",", Bio::MView::Manager::check_colormap), "\n"); } __DELETE_PARAM('def_con_colormap'); __PV; } OPTION: con_groupmap usage: "Name of groupmap to use if coloring by consensus" type: s param: con_groupmap convert: sub { __ARGS; if (defined __OV) { __PV = __OV; } else { __PV = __PARAM{'def_con_groupmap'}; } __PV = Bio::MView::Manager::check_groupmap(__PV); unless (defined __PV) { __WARN("unknown groupmap '-__ON=__OV'."); __WARN("known maps are: ", join(",", Bio::MView::Manager::check_groupmap), "\n"); } __DELETE_PARAM('def_con_groupmap'); __PV; } OPTION: con_threshold usage: "Consensus line thresholds" type: @f default: '100,90,80,70' param: con_threshold convert: sub { __ARGS; local $_; foreach (@{__PV}) { if ($_ < 50 or $_ > 100) { __WARN("bad range for '-__ON=$_' must be in range 50..100."); } } __PV; } OPTION: con_ignore usage: "Ignore singleton or class groups __CHOOSE(Bio::MView::Manager::check_ignore_class)" type: s default: none param: con_ignore convert: sub { __ARGS; __PV = Bio::MView::Manager::check_ignore_class(__OV); if (!defined __PV) { __WARN("unknown consensus ignore mode '-__ON=__OV'."); __WARN("known ignore classes are: ", join(",", Bio::MView::Manager::check_ignore_class), "\n"); } __PV; } ########################################################################### [HYBRID] text: "Hybrid alignment and consensus:" OPTION: con_gaps usage: "Count gaps during consensus computations if set to 'on'" type: b default: on param: ########################################################################### [MAPS] text: "User defined colormap and consensus group definition:" OPTION: colorfile usage: "Load more colormaps from file" OPTION: groupfile usage: "Load more groupmaps from file" ########################################################################### [GENERALFORMAT] text: "Miscellaneous formatting:" OPTION: gap usage: "Use this gap character" type: s default: - param: OPTION: label0 usage: "Switch off label {0= row number}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label1 usage: "Switch off label {1= identifier}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label2 usage: "Switch off label {2= description}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label3 usage: "Switch off label {3= scores}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label4 usage: "Switch off label {4= percent identity}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label5 usage: "Switch off label {5= first sequence positions: query}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: label6 usage: "Switch off label {6= second sequence positions: hit}" default: 0 param: convert: sub { __ARGS; (__OV ? 0 : 1) } OPTION: register usage: "Output multi-pass alignments with columns in register" type: b default: on param: ########################################################################### [HTML] text: "HTML markup:" OPTION: html usage: "Controls amount of HTML markup {head,body,data,full,off}" type: s default: off param: convert: sub { __ARGS; if (__OV =~ /^full/i) { __OPTION{__ON} = (16|8|4|2|1); return 1; } if (__OV =~ /^head/i) { __OPTION{__ON} = (8|4|2|1); return 1; } if (__OV =~ /^body/i) { __OPTION{__ON} = (4|2|1); return 1; } if (__OV =~ /^data/i) { __OPTION{__ON} = (1); return 1; } if (__OV =~ /^off/i) { __OPTION{__ON} = 0; return 0; } __WARN ("unknown setting '-__ON=__OV'"); } OPTION: title usage: "Page title string" type: s default: "" OPTION: pagecolor usage: "Page backgound color" type: s default: white OPTION: textcolor usage: "Page text color" type: s default: black OPTION: linkcolor usage: "Link color" type: s default: blue param: OPTION: alinkcolor usage: "Active link color" type: s default: red param: OPTION: vlinkcolor usage: "Visited link color" type: s default: purple param: OPTION: alncolor usage: "Alignment background color" type: s default: white param: OPTION: labcolor usage: "Alignment label color" type: s default: black param: OPTION: symcolor usage: "Alignment symbol default color" type: s default: #666666 param: OPTION: gapcolor usage: "Alignment gap color" type: s default: #666666 param: OPTION: css usage: "Use Cascading Style Sheets {off,on,URL}" type: s default: off param: css1 convert: sub { __ARGS; #supplied style sheet URL return 1 if __OV =~ /^(?:file|http):/i; if (__OV ne 'on' and __OV ne 'off' and __OV ne '0' and __OV ne '1') { __WARN("bad value for '-__ON=__OV' want {on,off,URL} or {0,1,URL}"); } return 1 if __OV eq 'on' or __OV eq '1'; return 0; } OPTION: bold usage: "Use bold emphasis for coloring sequence symbols" default: 0 param: convert: sub { __ARGS; __OV > 0 ? 1 : 0 } OPTION: srs usage: "Try to use SRS links {off,on}" type: s default: off action: sub { __ARGS; if (__OV eq 'off') { return $Bio::SRS::Type = 0; } elsif (__OV eq 'on') { return $Bio::SRS::Type = 1; } else { __WARN("bad SRS setting, want {off,on}."); } return $Bio::SRS::Type = 1; #default } OPTION: find usage: "Find and highlight exact string or simple regular expression or ':' delimited set of patterns" type: s default: "" param: action: sub { __ARGS; if (__OV) { __PARAM{'aln_coloring'} = 'find'; __PARAM{'aln_colormap'} = Bio::MView::Manager::get_default_find_colormap(); } } ########################################################################### [GENERICBLAST] OPTION: hsp type: s default: ranked param: convert: sub { __ARGS; return 'all' if __OV =~ /^a/; return 'discrete' if __OV =~ /^d/; return 'ranked' if __OV =~ /^r/; __WARN("bad setting '-__ON=__OV'."); __WARN("known hsp methods are: ", join(",", Bio::MView::Manager::check_hsp_tiling), "\n"); } OPTION: maxeval type: s default: unlimited param: convert: sub { __ARGS; return undef if __OV eq 'unlimited'; __TEST('f', __ON, __OV); __WARN("bad setting '-__ON=__OV', want > 0.") if __OV < 0; __OV; } OPTION: minbits type: s default: unlimited param: convert: sub { __ARGS; return undef if __OV eq 'unlimited'; __TEST('f', __ON, __OV); __WARN("bad setting '-__ON=__OV', want > 0.") if __OV < 0; __OV; } OPTION: strand type: @s default: both param: convert: sub { __ARGS; local $_; foreach (@{__PV}) { if (lc $_ eq 'p') { return ['+']; } elsif (lc $_ eq 'm') { return ['-']; } elsif (lc $_ eq 'both') { return []; } elsif ($_ eq '*') { return []; } else { __WARN("bad value for '-__ON=$_' choose from '{p,m,both,*}'"); } } } ########################################################################### [BLAST1] text: "NCBI BLAST (series 1):" #generic OPTION: hsp usage: "HSP tiling method __CHOOSE(Bio::MView::Manager::check_hsp_tiling)" type: s default: ranked OPTION: maxpval usage: "Ignore hits with p-value greater than N" type: s default: unlimited param: convert: sub { __ARGS; return undef if __OV eq 'unlimited'; __TEST('f', __ON, __OV); __WARN("bad setting '-__ON=__OV', want > 0.") if __OV < 0; __OV; } OPTION: minscore usage: "Ignore hits with score less than N" type: s default: unlimited param: convert: sub { __ARGS; return undef if __OV eq 'unlimited'; __TEST('f', __ON, __OV); __WARN("bad setting '-__ON=__OV', want > 0.") if __OV < 0; __OV; } #generic OPTION: strand usage: "Report only these query strand orientations {p,m,both,*}" type: @s default: both ########################################################################### [BLAST2] text: "NCBI BLAST (series 2), NCBI BLAST+, WashU-BLAST:" #generic OPTION: hsp usage: "HSP tiling method __CHOOSE(Bio::MView::Manager::check_hsp_tiling)" type: s default: ranked #generic OPTION: maxeval usage: "Ignore hits with e-value greater than N" type: s default: unlimited #generic OPTION: minbits usage: "Ignore hits with bits less than N" type: s default: unlimited #generic OPTION: strand usage: "Report only these query strand orientations {p,m,both,*}" type: @s default: both ########################################################################### [PSIBLAST] text: "NCBI PSI-BLAST:" #generic OPTION: hsp usage: "HSP tiling method __CHOOSE(Bio::MView::Manager::check_hsp_tiling)" type: s default: ranked #generic OPTION: maxeval usage: "Ignore hits with e-value greater than N" type: s default: unlimited #generic OPTION: minbits usage: "Ignore hits with bits less than N" type: s default: unlimited OPTION: cycle usage: "Process the N'th cycle of a multipass search {1..N,first,last,all,*}" type: @s default: last param: convert: sub { __ARGS; local $_; my @tmp=(); foreach (@{__PV}) { if ($_ eq 'first') { push @tmp, 1; } elsif ($_ eq 'last') { push @tmp, 0; } elsif ($_ eq 'all') { @tmp = (); last; } elsif ($_ eq '*') { @tmp = (); last; } elsif (/^\d+$/) { push @tmp, $_; } else { __WARN("bad value for '-__ON=$_' choose from '{1..N,first,last,all,*}'"); } } return [ @tmp ]; } ########################################################################### [FASTA] text: "FASTA (U. of Virginia):" OPTION: minopt usage: "Ignore hits with opt score less than N" type: s default: unlimited param: convert: sub { __ARGS; return undef if __OV eq 'unlimited'; __TEST('f', __ON, __OV); __WARN("bad setting '-__ON=__OV', want > 0.") if __OV < 0; __OV; } #generic OPTION: strand usage: "Report only these query strand orientations {p,m,both,*}" type: @s default: both ########################################################################### [HSSP] text: "HSSP/Maxhom:" OPTION: chain usage: "Report only these chainnames/numbers {A..B,1..N,first,last,all,*}" type: @s default: * param: convert: sub { __ARGS; local $_; my @tmp=(); foreach (@{__PV}) { if ($_ eq 'first') { push @tmp, 1; } elsif ($_ eq 'last') { push @tmp, 0; } elsif ($_ eq 'all') { @tmp = (); last; } elsif ($_ eq '*') { @tmp = (); last; } else { push @tmp, $_; } } return [ @tmp ]; } ########################################################################### [MAF] text: "UCSC MAF:" OPTION: block usage: "Report only these blocks {1..N,first,last,all,*}" type: @s default: first param: convert: sub { __ARGS; local $_; my @tmp=(); foreach (@{__PV}) { if ($_ eq 'first') { push @tmp, 1; } elsif ($_ eq 'last') { push @tmp, 0; } elsif ($_ eq 'all') { @tmp = (); last; } elsif ($_ eq '*') { @tmp = (); last; } elsif (/^\d+$/) { push @tmp, $_; } else { __WARN("bad value for '-__ON=$_' choose from '{1..N,first,last,all,*}'"); } } return [ @tmp ]; } ########################################################################### [MULTAL] text: "MULTAL/MULTAS:" #share OPTION: block usage: "Report only these blocks {1..N,first,last,all,*}" type: @s default: first ########################################################################### [HELP] text: "More information and help:" OPTION: help usage: "This help" OPTION: listcolors usage: "Print listing of known colormaps" OPTION: listgroups usage: "Print listing of known consensus groups" OPTION: listcss usage: "Print style sheet" ###########################################################################