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pal2nal.pl
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pal2nal.pl
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#!/usr/bin/perl
#
# pal2nal.pl (v14) Mikita Suyama
#
# Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options] > output
#
# pep.aln: protein alignment either in CLUSTAL or FASTA format
#
# nuc.fasta: DNA sequences (single multi-fasta or separated files)
#
# Options: -output (clustal(default)|paml|fasta|codon)
# -nogap
# -html
# -nostderr
# -blockonly
# -nomismatch
# -codontable N (default=1(universal))
#
# - IDs in pep.aln are used in the output.
#
# - Sequence order is automatically checked (see the comment of v12).
#
# - In-frame stop -> "*" or "_"
#
# - Frameshift
#
# Gene HCDG
# Pseudo HC1G 2 del in pseudo
#
# Gene HCDG
# Pseudo HC2G 1 del in pseudo
#
# Gene ND-TY
# Pseudo ND1TY 1 ins in pseudo
#
# Gene ND-TY
# Pseudo ND2TY 2 ins in pseudo
#
# Gene EREQK
# Pseudo EK4QK 1 ins in pseudo
#
#
# example:
#
# pep.aln
# AA1 ACDEFGARH1G-F*
# AA2 A2DDW-A*H-G2F*
#
# nuc.fasta
# >NUC1
# GCTTGTGATGAATTTGGTGCTCGTCATGGGGTTTTAA
# >NUC2
# GCGGGGACGACTGGGCGTAGCACGGGGGTTTTGA
#
# output
# NUC1 GCTTGTGATGAATTTGGTGCTCGTCATG--GGG---TTTTAA
# NUC2 GCGGG-GACGACTGG---GCGTAGCAC---GGGGG-TTTTGA
#
# v14.
# - NCBI GenBank codon table
# 1 Universal code
# 2 Vertebrate mitochondrial code
# 3 Yeast mitochondrial code
# 4 Mold, Protozoan, and Coelenterate Mitochondrial code
# and Mycoplasma/Spiroplasma code
# 5 Invertebrate mitochondrial
# 6 Ciliate, Dasycladacean and Hexamita nuclear code
# 9 Echinoderm and Flatworm mitochondrial code
# 10 Euplotid nuclear code
# 11 Bacterial, archaeal and plant plastid code
# 12 Alternative yeast nuclear code
# 13 Ascidian mitochondrial code
# 14 Alternative flatworm mitochondrial code
# 15 Blepharisma nuclear code
# 16 Chlorophycean mitochondrial code
# 21 Trematode mitochondrial code
# 22 Scenedesmus obliquus mitochondrial code
# 23 Thraustochytrium mitochondrial code
#
# - Initiation Met is treated separately.
# 2011/12/02
#
# v13.
# - file type (Win, UNIX, Mac)
# new-line:
# Win CR+LF \x0D\x0A
# UNIX LF \x0A
# Mac CR \x0D
#
# undef $/;
# s/\x0D\x0A|\x0D|\x0A/\n/g;
#
# OS: $^O
# 2010/07/26
#
# - run bl2seq for inconsistency check if it happens on linux.
# 2008/04/23
# v12.1
# - If there is a mismatch, the first atg(lower-case) couldn't
# recognized as Met.
# 2009/06/22
#
# v12.
# - About the input files:
# Now this script automatically check the following
# two possibilities:
# - If the same IDs are used in pep.aln and nuc.fasta,
# then you don't have to care about the order of
# the seqs.
# - If not,
# the same order of the seqs in pep.aln and nuc.fasta
# is assumed.
#
# - In case of 'inconsistency between...', run bl2seq if available
#
# - Some '1 while' replacement was very slow if the string
# very long (ca 10k). The routine is modified for speed-up.
#
# 02/02/2007
# v11.
# - Mac/DOS file (^M = \r).
#
# - bug fixed:
# If aa = '4' (frame shift), 'codon' output
# had 1 aa shift.
# 09/08/2006
# v10.
# - input DNA can be upper/lower cases
# (in older version, only upper case was allowed).
#
# - don't report warning if the first Met is GTG
#
# - default input aln type: clustal
# 01/08/2006
# v9.3.
# - "codon" was added to the output options.
# - if ($html), print "<pre>" and "</pre>".
# 20/06/2006
#
# v9.2.
# - pn2codon is modified (to v4)
# from: 10 residue window (incl '-')
# to: 10 residue window (excl '-')
# 19/06/2006
# v9.1.
# - to handle '/' followed by '*'
#
# $aaseq[$i] =~ s/\/(-*)[A-Z]/-${1}2/g;
# |
# v
# $aaseq[$i] =~ s/\/(-*)[A-Z\*]/-${1}2/g;
# 16/06/2006
# v9.
# - Frameshift in tfastx/tfasty
#
# \ -> +1
#
# / -> -1 (e.g. PG/A -> PG-2)
# 06/06/2006
# v8.
# - automatic detection of the input alignment format
# (-a is no longer used.)
# 14/02/2006
# - new option:
# -nomismatch -> remove mismatched codons (mismatch between
# pep and cDNA) from the output.
#
# -codontable (universal(default)|vmitochondria)
# 26/03/2006
# v7.
# - new option:
# # -a input_alignment_type
# # clustal (default) CLUSTALW format
# # fasta
# # gblocks Gblocks txt format *-gb.txt (-p=t)
# #
# # in the case of "-a gblocks", only the codons in conserved
# # blocks are converted into codon alignment.
# 27/01/2006
#
# - if clustal alignment contains
#
# - new option:
# -blockonly
# 03/02/2006
#
# - show warning message only if the position is marked '#'.
#
# - -i, -j options are deleted.
# 08/02/2006
# v6.
# # - new option:
# # -fasta -> set this option if input pep file is
# # not in *.aln format but in *.fasta format.
# # 16/08/2005
#
# v4.
# - new option:
# -html -> for the web server (STDERR messages -> STDOUT)
# (mismatch in color)
# -nostderr -> for Ks,Ka calc on the web server (NO STDERR messages)
# 25/04/2005
#
# v3.
# - renamed back to "pal2nal.pl"
# - subroutine (pn2codon) is modified:
# - reverse translation table (%p2c) was replaced
# - if there is no exact match, try fragment anchors
# - return value is changed to hash
# - new options:
# -output clustal|paml|fasta
# clustal format (default)
# paml
# fasta
# -nogap -> remove all gaped codons and stop codons
#
# 22/04/2005
# v2.
# - nuc.fasta can be either one multiple fasta file or several files.
# The order of seqs should be the same as those in the pep.aln file.
# 13/07/2004
#
# old script name: pal2nal.pl
# 06/09/2000 Mikita Suyama
#
# - modified for multiple seqs. 17/10/2000
#
# - AA-ids and NUC-ids must be the same -> TURNED OFF 05/05/2002
# Now, only the order is the matter.
# AA-ids are used throughout; NUC-ids are not used at all.
#
# - old condition: AA = NUC
# new condition: AA <= NUC ## NUC(cDNA) can be longer than AA ##
#
# - renamed from "pal2nal.pl" to codon_aln.pl 12/07/2004
#
$| = 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 = 1;
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 != 1 && $codontable != 2 && $codontable != 3 &&
$codontable != 4 && $codontable != 5 && $codontable != 6 &&
$codontable != 9 && $codontable != 10 && $codontable != 11 &&
$codontable != 12 && $codontable != 13 && $codontable != 14 &&
$codontable != 15 && $codontable != 16 && $codontable != 21 &&
$codontable != 22 && $codontable != 23) {
print STDERR "\nERROR: invalid codontable number, $codontable!!\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 ($codontable != 1) {
# push(@outmessage, "Codon table $codontable is used");
splice(@outmessage, 0, 0, "Codontable $codontable is used");
}
if (!$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) {