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Copy pathpal2nal.pl
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pal2nal.pl
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#!/usr/bin/perl
$| = 1;
undef $/;
$myos = $^O;
if ($#ARGV < 1) {
& showhelp();
exit;
} else {
$getoutform = 0;
$nogap = 0;
$html = 0;
$nostderr = 0;
$fasta = 0;
undef($alnfile);
undef(@nucfiles);
$outform = "clustal";
$blockonly = 0;
$nomismatch = 0;
$getcodontable = 0;
$codontable = "universal";
foreach $i (0..$#ARGV) {
if ($ARGV[$i] eq "-h") {
& showhelp();
} elsif ($ARGV[$i] eq "-output") {
$getoutform = 1;
} elsif ($getoutform) {
$outform = $ARGV[$i];
if ($outform ne "clustal" &&
$outform ne "paml" &&
$outform ne "fasta" &&
$outform ne "codon") {
print STDERR "\nERROR: valid output format: clustal, paml, fasta, or codon\n\n";
exit;
}
$getoutform = 0;
} elsif ($ARGV[$i] eq "-blockonly") {
$blockonly = 1;
} elsif ($ARGV[$i] eq "-nogap") {
$nogap = 1;
} elsif ($ARGV[$i] eq "-nomismatch") {
$nomismatch = 1;
} elsif ($ARGV[$i] eq "-codontable") {
$getcodontable = 1;
} elsif ($getcodontable) {
$codontable = $ARGV[$i];
if ($codontable ne "universal" &&
$codontable ne "vmitochondria") {
print STDERR "\nERROR: valid codon table: universal or vmitochondria\n\n";
exit;
}
$getcodontable = 0;
} elsif ($ARGV[$i] eq "-html") {
$html = 1;
} elsif ($ARGV[$i] eq "-nostderr") {
$nostderr = 1;
} elsif (!$alnfile) {
$alnfile = $ARGV[$i];
} else {
push(@nucfiles, $ARGV[$i]);
}
}
}
if ($html) {
print "<pre>\n";
}
#---------------#
# check options ("-outform codon" is not valid with -blockonly, -nogap, -nomismatch.)
#---------------#
if ($outform eq "codon" &&
($blockonly || $nogap || $nomismatch)) {
if ($html) {
print "\nERROR: if \"codon(Output format)\" is selected, don't use \"Remove gaps, inframe stop codons\" or \"Remove mismatches\" or \"Use only selected positions\".\n\n";
} else {
print STDERR "\nERROR: \"-outform codon\" is not valid with -blockonly, -nogap, -nomismatch\n\n";
}
exit;
}
#---------------------#
# Get nuc sequences
#---------------------#
undef(@nucid);
undef(%id2nucseq);
$nseq = -1;
foreach $i (0..$#nucfiles) {
open(NUCFILE, "< $nucfiles[$i]") || die "Can't open $nucfiles[$i]";
$nucfiledata = <NUCFILE>;
close(NUCFILE);
$nucfiledata =~ s/\x0D\x0A|\x0D|\x0A/\n/g;
foreach (split(/\n/, $nucfiledata)) {
if (!/^#/ && /\S+/) {
if (/^>(\S+)/) {
++$nseq;
$tmpnucid = $1;
push(@nucid, $tmpnucid);
} else {
s/[^a-zA-Z]//g;
$id2nucseq{$tmpnucid} .= $_;
}
}
}
}
#-------------------#
# Get aa alignemt
#-------------------#
undef(@aaid);
undef(%id2aaaln);
undef(%aaidcnt);
undef(@aaseq);
undef($gblockseq);
$gettype = 1;
open(ALNFILE, "< $alnfile") || die "Can't open $alnfile";
while (<ALNFILE>) {
chomp;
if ($gettype && !/^#/ && /\S+/) {
if (/^CLUSTAL/) {
$inalntype = "clustal";
} elsif (/^>/) {
$inalntype = "fasta";
} elsif (/^Gblocks/) {
$inalntype = "gblocks";
} else {
$inalntype = "clustal";
}
$gettype = 0;
}
}
close(ALNFILE);
open(ALNFILE, "< $alnfile") || die "Can't open $alnfile";
$getblock = 0;
$aafiledata = <ALNFILE>;
close(ALNFILE);
$aafiledata =~ s/\x0D\x0A|\x0D|\x0A/\n/g;
foreach (split(/\n/, $aafiledata)) {
if ($inalntype eq "clustal") {
if (!/^CLUSTAL/ && /^\S+/ && !/^#/) {
s/\s+$//;
@dat = split(/\s+/, $_);
++$aaidcnt{$dat[0]};
push(@aaid, $dat[0]) if ($aaidcnt{$dat[0]} == 1);
$dat[1] =~ tr/a-z/A-Z/;
$id2aaaln{$dat[0]} .= $dat[1];
$tmplen = length($_);
/^\S+\s+/;
$idspc = length($&);
$subalnlen = length($dat[1]);
$getblock = 1;
} elsif ($getblock) {
$_ .= ' ' x ($tmplen - length($_));
$gblockseq .= substr($_, $idspc, $subalnlen);
$getblock = 0;
}
} elsif ($inalntype eq "fasta") {
if (/^>(\S+)/) {
$tmpid = $1;
push(@aaid, $tmpid);
} else {
s/\s+//g;
tr/a-z/A-Z/;
$id2aaaln{$tmpid} .= $_;
}
} elsif ($inalntype eq "gblocks") {
$getaln = 0;
if (/^\s+\=/) {
$getaln = 1;
} elsif (/^Parameters/) {
$getaln = 0;
} elsif ($getaln) {
@dat = split(/\s+/, $_);
if (/^Gblocks/) {
$gblockseq .= $dat[1];
} elsif (/^\S+/) {
++$aaidcnt{$dat[0]};
push(@aaid, $dat[0]) if ($aaidcnt{$dat[0]} == 1);
$dat[1] =~ tr/a-z/A-Z/;
$id2aaaln{$dat[0]} .= $dat[1];
}
}
}
}
foreach $i (0..$#aaid) {
push(@aaseq, $id2aaaln{$aaid[$i]});
}
#------------------------------------#
# For frameshifts in tfastx/tfasty
#------------------------------------#
foreach $i (0..$#aaid) {
$aaseq[$i] =~ s/\\/1/g;
$aaseq[$i] =~ s/\/(-*)[A-Z\*]/-${1}2/g;
}
#-------------------------------------#
# Check the input seqs (pep <=> nuc)
#-------------------------------------#
if ($#aaid != $#nucid) {
$naa = $#aaid + 1;
$nnuc = $#nucid + 1;
if ($html) {
print "\nERROR: number of input seqs differ (aa: $naa; nuc: $nnuc)!!\n\n";
} else {
print STDERR "\nERROR: number of input seqs differ (aa: $naa; nuc: $nnuc)!!\n\n";
print STDERR " aa '@aaid'\n";
print STDERR " nuc '@nucid'\n";
}
exit;
}
#---------------------------------#
# corresponding IDs or same order
#---------------------------------#
@commonids = & common_elem(*aaid, *nucid);
sub common_elem {
local(*aarr, *barr) = @_;
local(%mark, @comarr);
grep($mark{$_}++, @aarr);
@comarr = grep($mark{$_}, @barr);
}
if ($#commonids == $#aaid) {
$idcorrespondence = "sameID";
} else {
$idcorrespondence = "ordered";
}
#-------------------#
# Codon sequences
#-------------------#
undef(@codonseq);
undef(%aaidpos2mismatch);
undef(@outmessage);
foreach $i (0..$#aaid) {
if ($idcorrespondence eq "sameID") {
$tmpnucid = $aaid[$i];
} elsif ($idcorrespondence eq "ordered") {
$tmpnucid = $nucid[$i];
} else {
print STDERR "\nERROR in ID correspondence.\n\n";
exit;
}
%codonout = & pn2codon($aaseq[$i], $id2nucseq{$tmpnucid}, $codontable);
@message = @{$codonout{'message'}};
foreach $j (0..$#message) {
$outl = "WARNING: $aaid[$i] $message[$j]";
push(@outmessage, $outl);
@dat = split(/\s+/, $message[$j]);
$dat[1] =~ s/:$//;
$aaidpos2mismatch{"$aaid[$i] $dat[1]"} = 1;
}
if ($codonout{'result'} == 1 || $codonout{'result'} == 2) {
push(@codonseq, $codonout{'codonseq'});
} else {
$erraa = $aaseq[$i];
$erraa =~ s/-//g;
# 1 while $erraa =~ s/(.{60})(.+)/$1\n$2/;
@frags = & my1while($erraa, 60);
$erraa = join("\n", @frags);
$errnuc = $id2nucseq{$tmpnucid};
$errnuc =~ s/-//g;
# 1 while $errnuc =~ s/(.{60})(.+)/$1\n$2/;
@frags = & my1while($errnuc, 60);
$errnuc = join("\n", @frags);
if ($html) {
print "</pre>\n";
print "<H1>ERROR in your input files!</H1>\n";
print "<pre>\n";
print "#--- ERROR: inconsistency between the following pep and nuc seqs ---#\n";
print ">$aaid[$i]\n";
print "$erraa\n";
print ">$tmpnucid\n";
print "$errnuc\n";
print "</pre>\n";
$tmpwhich = "tmp/tmpwhich.$$";
} else {
print STDERR "#--- ERROR: inconsistency between the following pep and nuc seqs ---#\n";
print STDERR ">$aaid[$i]\n";
print STDERR "$erraa\n";
print STDERR ">$tmpnucid\n";
print STDERR "$errnuc\n";
$tmpwhich = "tmpwhich.$$";
}
if ($myos eq "linux") {
system("which bl2seq > $tmpwhich");
$foundbl2seq = 0;
open(TMPWHICH, "< $tmpwhich") || die "Can't open $tmpwhich";
while (<TMPWHICH>) {
chomp;
$foundbl2seq = 1 if (/bl2seq$/);
}
close(TMPWHICH);
unlink($tmpwhich);
if ($foundbl2seq) {
#------------------------------------------#
# run bl2seq (if the command is available)
#------------------------------------------#
if ($html) {
$erraafile = "tmp/erraafile.$$";
$errnucfile = "tmp/errnucfile.$$";
$tblnout = "tmp/tbln.out.$$";
} else {
$erraafile = "erraafile.$$";
$errnucfile = "errnucfile.$$";
$tblnout = "tbln.out.$$";
}
open(ERRAAFILE, "> $erraafile") || die "Can't open $erraafile";
print ERRAAFILE ">$aaid[$i]\n";
print ERRAAFILE "$erraa\n";
close(ERRAAFILE);
open(ERRNUCFILE, "> $errnucfile") || die "Can't open $errnucfile";
print ERRNUCFILE ">$tmpnucid\n";
print ERRNUCFILE "$errnuc\n";
close(ERRNUCFILE);
system("bl2seq -p tblastn -F F -i $erraafile -j $errnucfile -o $tblnout");
if ($html) {
print "<BR>\n";
print "<BR>\n";
print "<H1>Check the following TBLASTN output.</H1><BR>\n";
print "<pre>\n";
print " your pep -> 'Query'\n";
print " your nuc -> 'Sbjct'\n";
print "<BR>\n";
} else {
print STDERR "\n";
print STDERR "\n";
print STDERR " ###----- Check the following TBLASTN output: -----###\n";
print STDERR " ###----- your pep -> 'Query' -----###\n";
print STDERR " ###----- your nuc -> 'Sbjct' -----###\n";
print STDERR "\n";
}
open(TBLNOUT, "< $tblnout") || die "Can't open $tblnout";
$tblnoutdata = <TBLNOUT>;
close(TBLNOUT);
$tblnoutdata =~ s/\x0D\x0A|\x0D|\x0A/\n/g;
foreach (split(/\n/, $tblnoutdata)) {
if ($html) {
print "$_\n";
} else {
print STDERR "$_\n";
}
}
if ($html) {
print "</pre>\n";
}
unlink($erraafile);
unlink($errnucfile);
unlink($tblnout);
} else {
if ($html) {
print "<BR>\n";
print "<BR>\n";
print "Run bl2seq (-p tblastn) or GeneWise to see the inconsistency.<BR>\n";
print "<BR>\n";
} else {
print STDERR "\n";
print STDERR "\n";
print STDERR "Run bl2seq (-p tblastn) or GeneWise to see the inconsistency.\n";
print STDERR "\n";
}
}
} else { #### non-linux environment
print STDERR "\n";
print STDERR "\n";
print STDERR "Run bl2seq (-p tblastn) or GeneWise to see the inconsistency.\n";
print STDERR "\n";
}
exit;
}
}
#-------------------#
# Warning in '#'?
#-------------------#
if ($gblockseq =~ /#/ && $blockonly) {
undef(@newoutmessage);
foreach $i (0..$#outmessage) {
$mpos = (split(/\s+/, $outmessage[$i]))[3];
$mpos =~ s/://;
if (substr($gblockseq, $mpos - 1, 1) eq "#") {
push(@newoutmessage, $outmessage[$i]);
}
}
@outmessage = @newoutmessage;
}
#--------------------#
# Warning messages
#--------------------#
if (!$nostderr) {
foreach $j (0..$#outmessage) {
if ($html) {
if ($j == 0 && !$nomismatch) {
print "#------------------------------------------------------------------------#\n";
}
if ($nomismatch) {
# print "# $outmessage[$j] (excluded from the output)\n";
} else {
print "# $outmessage[$j]\n";
}
if ($j == $#outmessage && !$nomismatch) {
print "#------------------------------------------------------------------------#\n\n";
}
} else {
if ($j == 0 && !$nomismatch) {
print STDERR "#------------------------------------------------------------------------#\n";
print STDERR "# Input files: $alnfile @nucfiles\n";
}
if ($nomismatch) {
# print STDERR "# $outmessage[$j] (exlucded from the output)\n";
} else {
print STDERR "# $outmessage[$j]\n";
}
if ($j == $#outmessage && !$nomismatch) {
print STDERR "#------------------------------------------------------------------------#\n\n";
}
}
}
}
undef(%errorpos);
foreach $j (0..$#outmessage) {
@dat = split(/\s+/, $outmessage[$j]);
$tmperrpos = $dat[3];
$tmperrpos =~ s/:$//;
$tmperrpos -= 1;
$errorpos{$tmperrpos} = 1;
}
#----------------------------------#
# Make an AA-based NUC alignment
#----------------------------------#
undef(@tmppos);
undef(@codonaln);
undef(@coloraln);
undef($maskseq);
foreach $i (0..length($aaseq[0]) - 1) {
$tmpmax = 0;
$apos = $i + 1;
#-----------#
# gblocks ?
#-----------#
$putcodon = 1;
if ($gblockseq =~ /#/ && substr($gblockseq, $i, 1) ne "#" && $blockonly) {
$putcodon = 0;
}
if ($nomismatch && $errorpos{$i}) {
$putcodon = 0;
}
foreach $k (0..$#aaid) {
$tmpaa = substr($aaseq[$k], $i, 1);
if ($tmpaa !~ /\d/) {
$tmplen = 3;
} else {
$tmplen = (int(($tmpaa - 1) / 3) + 1) * 3; # 1, 2, 3 -> 3
# 4, 5, 6 -> 6
# 7, 8, 9 -> 9
}
$tmpmax = $tmplen if ($tmpmax < $tmplen);
}
foreach $k (0..$#aaid) {
$tmpaa = substr($aaseq[$k], $i, 1);
if ($tmpaa !~ /\d/) {
if ($tmpaa eq '-') {
# if ($putcodon || (!$blockonly && !$nomismatch)) {
if ($putcodon) {
$codonaln[$k] .= '-' x $tmpmax;
if ($aaidpos2mismatch{"$aaid[$k] $apos"}) {
$coloraln[$k] .= 'R' x $tmpmax;
} else {
$coloraln[$k] .= '-' x $tmpmax;
}
}
} elsif ($tmpaa =~ /[A-Z]/ || $tmpaa eq '*') {
# if ($putcodon || (!$blockonly && !$nomismatch)) {
if ($putcodon) {
$codonaln[$k] .= substr($codonseq[$k], $tmppos[$k], 3);
if ($aaidpos2mismatch{"$aaid[$k] $apos"}) {
$coloraln[$k] .= 'RRR';
} else {
$coloraln[$k] .= '---';
}
}
$tmppos[$k] += 3;
# if ($putcodon || (!$blockonly && !$nomismatch)) {
if ($putcodon) {
$codonaln[$k] .= '-' x ($tmpmax - 3) if ($tmpmax - 3 > 0);
if ($aaidpos2mismatch{"$aaid[$k] $apos"}) {
$coloraln[$k] .= 'R' x ($tmpmax - 3) if ($tmpmax - 3 > 0);
} else {
$coloraln[$k] .= '-' x ($tmpmax - 3) if ($tmpmax - 3 > 0);
}
}
}
} elsif ($tmpaa =~ /\d/) {
# if ($putcodon || (!$blockonly && !$nomismatch)) {
if ($putcodon) {
$codonaln[$k] .= substr($codonseq[$k], $tmppos[$k], $tmpaa);
if ($aaidpos2mismatch{"$aaid[$k] $apos"}) {
$coloraln[$k] .= 'R' x $tmpaa;
} else {
$coloraln[$k] .= '-' x $tmpaa;
}
}
$tmppos[$k] += $tmpaa;
# if ($putcodon || (!$blockonly &&!$nomismatch)) {
if ($putcodon) {
$codonaln[$k] .= '-' x ($tmpmax - $tmpaa);
if ($aaidpos2mismatch{"$aaid[$k] $apos"}) {
$coloraln[$k] .= 'R' x ($tmpmax - $tmpaa);
} else {
$coloraln[$k] .= '-' x ($tmpmax - $tmpaa);
}
}
}
}
if (!$blockonly) {
# if ($putcodon && substr($gblockseq, $i, 1) eq "#") {
# $maskseq .= '#' x $tmpmax;
# } else {
# $maskseq .= ' ' x $tmpmax;
# }
if ($putcodon) {
if (substr($gblockseq, $i, 1) eq "#") {
$maskseq .= "#" x $tmpmax;
} else {
$maskseq .= " " x $tmpmax;
}
}
}
}
#-----------#
# -nogap?
#-----------#
$alilen = length($codonaln[0]);
if ($nogap) {
$tmppos = 0;
undef(@nogapaln);
undef(@nogapcoloraln);
undef($nogapmaskseq);
while ($tmppos < $alilen) {
$outok = 1;
foreach $i (0..$#codonaln) {
$tmpcodon = substr($codonaln[$i], $tmppos, 3);
$outok = 0 if ($tmpcodon =~ /-/);
$outok = 0 if ($tmpcodon =~ /(((U|T)A(A|G|R))|((T|U)GA))/);
}
if ($outok) {
foreach $i (0..$#codonaln) {
$tmpcodon = substr($codonaln[$i], $tmppos, 3);
$nogapaln[$i] .= $tmpcodon;
$tmpcolorcodon = substr($coloraln[$i], $tmppos, 3);
$nogapcoloraln[$i] .= $tmpcolorcodon;
}
$nogapmaskseq .= substr($maskseq, $tmppos, 3);
}
$tmppos += 3;
}
@codonaln = @nogapaln;
@coloraln = @nogapcoloraln;
$maskseq = $nogapmaskseq;
}
#----------#
# Output
#----------#
$maxn = 0;
foreach $i (0..$#aaid) {
$maxn = length($aaid[$i]) if ($maxn < length($aaid[$i]));
}
$maxn = 10 if ($maxn < 10);
$alilen = length($codonaln[0]);
# foreach $i (0..$#aaid) {
# 1 while $codonaln[$i] =~ s/(.{60})(.+)/$1\n$2/;
# 1 while $coloraln[$i] =~ s/(.{60})(.+)/$1\n$2/;
# }
# 1 while $maskseq =~ s/(.{60})(.+)/$1\n$2/;
undef(%aaid2codonarr);
undef(%aaid2colorarr);
foreach $i (0..$#aaid) {
@{$aaid2codonarr{$aaid[$i]}} = & my1while($codonaln[$i], 60);
@{$aaid2colorarr{$aaid[$i]}} = & my1while($coloraln[$i], 60);
}
@maskarr = & my1while($maskseq, 60);
if ($outform eq "clustal") {
#-----------#
# clustal
#-----------#
print "CLUSTAL W multiple sequence alignment\n";
print "\n";
@output1 = @{$aaid2codonarr{$aaid[0]}};
if ($html) {
foreach $i (0..$#output1) {
foreach $k (0..$#aaid) {
printf "%-${maxn}s ", $aaid[$k];
$outf = ${$aaid2codonarr{$aaid[$k]}}[$i];
$outr = ${$aaid2colorarr{$aaid[$k]}}[$i];
$rlen = length($outf);
if ($outr =~ /R/) {
foreach $l (0..$rlen - 1) {
$tmpnuc = substr($outf, $l, 1);
$tmpr = substr($outr, $l, 1);
if ($tmpr eq "R") {
print "<FONT color='red'>$tmpnuc</FONT>";
} else {
print "$tmpnuc";
}
}
print "\n";
} else {
print "$outf\n";
}
}
$outmask = $maskarr[$i];
printf "%-${maxn}s $outmask\n", ' ' if (!$blockonly && $gblockseq =~ /#/);
print "\n";
}
} else {
foreach $i (0..$#output1) {
foreach $k (0..$#aaid) {
$outf = ${$aaid2codonarr{$aaid[$k]}}[$i];
printf "%-${maxn}s $outf\n", $aaid[$k];
}
$outmask = $maskarr[$i];
printf "%-${maxn}s $outmask\n", ' ' if (!$blockonly && $gblockseq =~ /#/);
print "\n";
}
}
} elsif ($outform eq "codon") {
#-------#
# codon
#-------#
# @outaa = @aaseq;
undef(@outaa);
$withn = 0;
foreach $j (0..$#aaid) {
$withn = 1 if ($aaseq[$j] =~ /\d/);
}
if ($withn) {
$alnlen = length($aaseq[0]);
foreach $i (0..$alnlen - 1) {
$maxaan = 0;
foreach $j (0..$#aaid) {
$tmpaa = substr($aaseq[$j], $i, 1);
if ($tmpaa =~ /\d/ && $tmpaa > $maxaan) {
$maxaan = $tmpaa;
}
}
if ($maxaan >= 4) {
$tmplen = int(($tmpaa - 1) / 3) + 1; # 4, 5, 6 -> 2
# 7, 8, 9 -> 3
} else {
$tmplen = 1;
}
foreach $j (0..$#aaid) {
$pushaa = '-' x $tmplen;
$tmpaa = substr($aaseq[$j], $i, 1);
substr($pushaa, 0, 1) = $tmpaa;
$outaa[$j] .= $pushaa;
}
}
} else {
@outaa = @aaseq;
}
undef(%aaid2aaarr);
foreach $i (0..$#aaid) {
# 1 while $outaa[$i] =~ s/(.{20})(.+)/$1\n$2/;
@{$aaid2aaarr{$aaid[$i]}} = & my1while($outaa[$i], 20);
}
@output1 = @{$aaid2codonarr{$aaid[0]}};
if ($html) {
foreach $i (0..$#output1) {
foreach $k (0..$#aaid) {
printf "%-${maxn}s ", '';
$outa = ${$aaid2aaarr{$aaid[$k]}}[$i];
# 1 while $outa =~ s/(\S)(\S+)/$1 $2/;
@frags = & my1while($outa, 1);
$outa = join(" ", @frags);
$outf = ${$aaid2codonarr{$aaid[$k]}}[$i];
# 1 while $outf =~ s/(\S{3})(\S+)/$1 $2/;
@frags = & my1while($outf, 3);
$outf = join(" ", @frags);
$outr = ${$aaid2colorarr{$aaid[$k]}}[$i];
# 1 while $outr =~ s/(\S{3})(\S+)/$1 $2/;
@frags = & my1while($outr, 3);
$outr = join(" ", @frags);
if ($outr =~ /R/) {
$rlen = length($outf);
foreach $l (0..$rlen - 1) {
$tmppep = substr($outa, $l, 1);
$tmpr = substr($outr, $l, 1);
if ($tmpr eq "R") {
print "<FONT color='red'>$tmppep</FONT>";
} else {
print "$tmppep";
}
}
print "\n";
printf "%-${maxn}s ", $aaid[$k];
foreach $l (0..$rlen - 1) {
$tmpnuc = substr($outf, $l, 1);
$tmpr = substr($outr, $l, 1);
if ($tmpr eq "R") {
print "<FONT color='red'>$tmpnuc</FONT>";
} else {
print "$tmpnuc";
}
}
print "\n";
} else {
print "$outa\n";
printf "%-${maxn}s ", $aaid[$k];
print "$outf\n";
}
}
$outmask = $maskarr[$i];
$outmask =~ s/\s/-/g;
# 1 while $outmask =~ s/(\S{3})(\S+)/$1 $2/;
@frags = & my1while($outmask, 3);
$outmask = join(" ", @frags);
$outmask =~ s/-/ /g;
printf "%-${maxn}s $outmask\n", ' ' if (!$blockonly && $gblockseq =~ /#/);
print "\n";
}
} else {
foreach $i (0..$#output1) {
foreach $k (0..$#aaid) {
$outa = ${$aaid2aaarr{$aaid[$k]}}[$i];
# 1 while $outa =~ s/(\S)(\S+)/$1 $2/;
@frags = & my1while($outa, 1);
$outa = join(" ", @frags);
printf "%-${maxn}s $outa\n", '';
$outf = ${$aaid2codonarr{$aaid[$k]}}[$i];
# 1 while $outf =~ s/(\S{3})(\S+)/$1 $2/;
@frags = & my1while($outf, 3);
$outf = join(" ", @frags);
printf "%-${maxn}s $outf\n", $aaid[$k];
}
$outmask = $maskarr[$i];
$outmask =~ s/\s/-/g;
# 1 while $outmask =~ s/(\S{3})(\S+)/$1 $2/;
@frags = & my1while($outmask, 3);
$outmask = join(" ", @frags);
$outmask =~ s/-/ /g;
printf "%-${maxn}s $outmask\n", ' ' if (!$blockonly && $gblockseq =~ /#/);
print "\n";
}
}
} elsif ($outform eq "paml") {
#--------#
# paml
#--------#
$nseq = $#aaid + 1;
printf " %3d %6d\n", $nseq, $alilen;
foreach $i (0..$#aaid) {
print "$aaid[$i]\n";
if ($html) {
@outf = @{$aaid2codonarr{$aaid[$i]}};
@outr = @{$aaid2colorarr{$aaid[$i]}};
foreach $k (0..$#outf) {
if ($outr[$k] =~ /R/) {
$lenf = length($outf[$k]);
foreach $l (0..$lenf - 1) {
$tmpnuc = substr($outf[$k], $l, 1);
$tmpr = substr($outr[$k], $l, 1);
if ($tmpr eq "R") {
print "<FONT color='red'>$tmpnuc</FONT>";
} else {
print "$tmpnuc";
}
}
print "\n";
} else {
print "$outf[$k]\n";
}
}
} else {
$outcodon = join("\n", @{$aaid2codonarr{$aaid[$i]}});
print "$outcodon\n";
}
}
} elsif ($outform eq "fasta") {
#---------#
# fasta
#---------#
foreach $i (0..$#aaid) {
print ">$aaid[$i]\n";
if ($html) {
@outf = @{$aaid2codonarr{$aaid[$i]}};
@outr = @{$aaid2colorarr{$aaid[$i]}};
foreach $k (0..$#outf) {
if ($outr[$k] =~ /R/) {
$lenf = length($outf[$k]);
foreach $l (0..$lenf - 1) {
$tmpnuc = substr($outf[$k], $l, 1);
$tmpr = substr($outr[$k], $l, 1);
if ($tmpr eq "R") {
print "<FONT color='red'>$tmpnuc</FONT>";
} else {
print "$tmpnuc";
}
}
print "\n";
} else {
print "$outf[$k]\n";
}
}
} else {
$outcodon = join("\n", @{$aaid2codonarr{$aaid[$i]}});
print "$outcodon\n";
}
}
}
if ($html) {
print "</pre>\n";
}
#-----------------------------------------------------------------------
sub pn2codon {
# pn2codon v4
#
# input: $pep protein sequence
# termination -> "_" or "*";
# frameshift -> digit
# "-" or "." -> gap
# $nuc DNA or RNA sequence (lower/upper case letters)
#
# $codontable 'universal' or 'vmitochondria'
#
# return: hash
# $retval{'codonseq'}: codon seq (w/o gap)
# $retval{'message'}: error/warning messame (array)
# $retval{'result'}: 1: OK, 2: mismatch, -1: no match found
#
#
# 05/05/2002 Mikita Suyama
# 12/07/2004
#
# v2 22/04/2005
# - reverse translation table (%p2c) was replaced
# - if there is no exact match, try fragment anchors
# - return value is changed to hash
#
# v3 26/03/2006
# - codon table for vertebrate mitochondria (vmitochondria) is added
#
# v4
# - from: 10 residue window (incl '-')
# to: 10 residue window (excl '-')
# 19/06/2006
# v5
# - bug fix:
# just before 'does not correspond'
# /$p2c{$tmpaa}/ -> /$p2c{$tmpaa}/i
# ^
# - the first Met can be (A|G|C|R)TG
# 01/08/2006
# v5.1
# - but fix:
# if ($tmpcodon !~ /((A|C|G|R)TG)/i) {
# ^
# 2009/06/22
#
local($pep, $nuc, $codontable) = @_;
local(%p2c);
local($peplen, $qcodon, $codon);
local($tmpaa, $message, $modpep, @qcodon, @fncodon, $wholecodon);
local($i, $j, $anclen, @anchor, $peppos, $tmpcodon, $codonpos);
local(%retval);
if ($codontable eq "universal") {
#-----------#
# universal
#-----------#
%p2c = (
"L" => "((C(U|T).)|((U|T)(U|T)(A|G|R)))",
"R" => "((CG.)|(AG(A|G|R)))",
"S" => "(((U|T)C.)|(AG(U|T|C|Y)))",
"A" => "(GC.)",
"G" => "(GG.)",
"P" => "(CC.)",
"T" => "(AC.)",
"V" => "(G(U|T).)",
"I" => "(A(U|T)(U|T|C|Y|A))",
"_" => "(((U|T)A(A|G|R))|((T|U)GA))",
"*" => "(((U|T)A(A|G|R))|((T|U)GA))",
"C" => "((U|T)G(U|T|C|Y))",
"D" => "(GA(U|T|C|Y))",
"E" => "(GA(A|G|R))",
"F" => "((U|T)(U|T)(U|T|C|Y))",
"H" => "(CA(U|T|C|Y))",
"K" => "(AA(A|G|R))",
"N" => "(AA(U|T|C|Y))",
"Q" => "(CA(A|G|R))",
"Y" => "((U|T)A(U|T|C|Y))",
"M" => "(A(U|T)G)",
"W" => "((U|T)GG)",
"X" => "...",
);
} elsif ($codontable eq "vmitochondria") {