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use strict;
use FileHandle;
use Bio::SeqIO;
use Bio::AlignIO;
my $MSA=shift;
my $OutTree=shift;
my $WorkingDir=shift;
my $Model=shift; #Available AA substitution models: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, GTR
#NUC: GTRCAT
my $MSA_Name=$MSA; # IF WITHOUT PATH
if ($MSA=~/([^\/]+)$/){$MSA_Name=$1;} # NAME WITHOUT PATH
my $OutTree_Suffix=$OutTree; # IF WITHOUT PATH
if ($OutTree=~/([^\/]+)$/){$OutTree_Suffix=$1;} # NAME WITHOUT PATH
$WorkingDir=$WorkingDir."/" if ($WorkingDir!~/\//);
my $Codes2NameIndex=$WorkingDir."$MSA_Name"."Codes2NamesIndex.txt";
my $CodedMSA=$WorkingDir."/$MSA_Name".".coded.aln";
my $CodedMSAPhylip=$WorkingDir."$MSA_Name".".coded.Phylip";
# Convert Names to numbers
my $ans=name2codeFastaFrom1("$MSA",$Codes2NameIndex,$CodedMSA);
#if ($ans ne "ok") {exit_on_error}
# Convert To Phylip
convertMsaFormat($CodedMSA,$CodedMSAPhylip,"fasta","phylip");
#my $convert_cmd="readseq -a -f12 $CodedMSA > $CodedMSAPhylip";
#system ($convert_cmd);
# Run RaxML
$Model="PROTCAT".$Model if ($Model ne "GTRCAT");
my $RaxML_cmd="cd $WorkingDir;raxmlHPC -s $CodedMSAPhylip -n $OutTree_Suffix"." -m $Model";
print "$RaxML_cmd\n";
system ($RaxML_cmd);
# Bring Back names to tree
my $RaxMLTree="RAxML_bestTree.$OutTree_Suffix";
code2nameTree($Codes2NameIndex,$WorkingDir.$RaxMLTree,$WorkingDir."$OutTree_Suffix");
sub name2codeFastaFrom1 {
####################################################################################################################
# Convert the names in a fasta file to numbers, and creates a code file with the names and the codes (running number)
###################################################################################################################
my $in_fileName = shift;
my $code_fileName = shift;
my $out_fileName = shift;
my $counter_offset=shift; # optional
my $in_file = Bio::SeqIO->new(-file => $in_fileName , '-format' => 'Fasta');
my $code_file = new FileHandle(">$code_fileName") or return ("Can't write to $code_fileName $!");
my $out_file = new FileHandle(">$out_fileName") or return ("Can't write to $out_fileName");
$counter_offset=1 if (!defined $counter_offset);
$counter_offset=1 if ($counter_offset==0);
my $counter = $counter_offset;
my $i;
while ( my $seqObj = $in_file->next_seq() ) {
my $name = $seqObj->display_id();
$name.= " ".$seqObj->desc() if ($seqObj->desc());
print $code_file "$name\t$counter\n";
my $seq = $seqObj->seq();
print $out_file ">$counter\n";
for($i=0;$i<length($seq);$i+=60){
print $out_file substr($seq,$i,60) . "\n";
}
if($i<length($seq)){
print $out_file substr($seq,$i,length($seq)-$i);
}
print $out_file "\n";
$counter++;
}
$out_file->close();
$in_file->close();
$code_file->close();
return "ok";
}
sub code2nameTree
{
###############################################################################################################
# Works together (or rather after) the script names2codeFasta.pl. Takes a tree created based on
# a fasta file with codes, and reverts the codes to the names. Required input is a code file which is created by
# names2codeFasta.pl
# ** very useful for working with all phyml and such, since these programs chop the name to 10 chars
###############################################################################################################
# die "Usage: code2name.pl CODE_FILE TREE_FILE NEW_FILE NAME_LENGTH" if (scalar(@ARGV) < 3);
my $nameLength = "NA";
my $code2nameFile = shift;
my $treeFile = shift;
my $newFile = shift;
$nameLength = shift;
if (!defined $nameLength) {
$nameLength = 30;
}
my %names2code;
my @fields;
open FH, "<$code2nameFile";
while (my $line=<FH>){
$line =~ /(.+)\t(\d+)/;
my $code = $2;
my $name = $1;
$name =~ s/[\[\]\,\:\;\(\)]/_/g; #remove characters that are newick format associated
if ($name =~ m/(.*\|.{$nameLength})/) {
$name = $1;
}
$names2code{$code}=$name;
print "$code $name\n";
}
close FH;
open TREE, "<$treeFile";
open NEWTREE, ">$newFile";
my $full_tree = "";
my $line2;
while ($line2 = <TREE>){ # this assumes there are bootstrap values on the input tree
chomp $line2;
$full_tree.=$line2;
}
@fields = split(/:/, $full_tree);
foreach my $field (@fields) {
if ($field =~ /[\,\(](\d+)$/) { # a leaf comes either after a "(" or a ","
$field =~ s/(\d+)$/$names2code{$1}/;
}
if ($field !~/;$/) {print NEWTREE "$field:";}
else {print NEWTREE "$field";} # Last One
}
print NEWTREE "\n";
}
sub convertMsaFormat
{
my $inFile=shift;
my $outFile=shift;
my $inFormat=shift;
my $outFormat=shift;
#die "usage: convertMsaFormat.pl <inFile> <outFile> <inFormat> <outFormat>\n"
print "inFile = '$inFile'\n";
print "outFile = '$outFile'\n";
print "inFormat = '$inFormat'\n";
print "outFormat = '$outFormat'\n";
my $in = Bio::AlignIO->new( '-format' => $inFormat , -file => $inFile);
my $out = Bio::AlignIO->new( '-format' => $outFormat , -file => ">$outFile");
my ($alignObj, $seqStr, $trans);
while ($alignObj = $in->next_aln()) {
$alignObj->verbose(1);
# Otherwise, bioperl adds sequence start/stop values, causing problems
# with clustal/bali_score
$alignObj->set_displayname_flat();
$out->write_aln($alignObj);
}
}
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