/usr/share/librg-utils-perl/blast2saf.pl is in librg-utils-perl 1.0.43-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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use Carp qw| cluck :DEFAULT |;
use File::Basename qw||;
#
$scrName=__FILE__;$scrName=~s/^.*\/|\.pl//g;
$scrGoal="converts blastpgp output file into saf (optional Rdb)".
" \t \n".
" \t ";
#
#
#
#------------------------------------------------------------------------------#
# Copyright 2000 #
# Dariusz Przybylski dudek@cubic.bioc.columbia.edu #
# Burkhard Rost rost@columbia.edu #
# CUBIC (Columbia Univ) http://cubic.bioc.columbia.edu/ #
# Dept Biochemistry & Molecular Biophysics #
# 650 West, 168 Street #
# New York, NY 10032 #
# version 1.0 Sep, 2000 #
#------------------------------------------------------------------------------#
#
&helpLocal() if ($#ARGV<0 || $ARGV[0]=~/^(-h|help|\?|def)$/i);
if ($#ARGV < 0) { die( "*** ERROR blastpgp_to_saf.pl : no arguments given"); }
#$fileErr="b2saf.tmp_".$$;
#open(FHERROR, ">$fileErr") || die "*** could not open error log file \n";
INI:{
$par{"extSaf"}= ".saf";
$par{"extRdb"}= ".rdbBlast";
$par{"extFasta"}=".f";
}
foreach $arg (@ARGV){
#if ($arg=~/^blast=(.*)$/) { $fileInBlast = $1;}
if ($arg=~/^fasta=(.*)$/) { $fileInQuery = $1;}
elsif ($arg=~/^saf=(.*)$/) { $fileOutSaf = $1;}
elsif ($arg=~/^rdb=(.*)$/) { $fileOutRdb = $1;}
elsif ($arg=~/^rdb$/) { $fileOutRdb = 1;}
elsif ($arg=~/^short$/) { $short = 1;}
elsif ($arg=~/^red=(.*)$/) { $filterThre = $1;}
elsif ($arg=~/^maxAli=(.*)$/) { $maxAli = $1;}
elsif ($arg=~/^tile=(.*)$/) { $alignTiling = $1;}
elsif ($arg=~/^eSaf=(.*)$/) { $eThresh = $1;}
elsif ($arg=~/^extSaf=(.*)$/) { $par{"extSaf"} = $1;}
elsif ($arg=~/^extFasta=(.*)$/) { $par{"extFasta"}= $1;}
elsif ($arg=~/^extRdb=(.*)$/) { $par{"extRdb"} = $1;}
elsif ($arg=~/^debug=(.*)$/) { $par{"debug"} = $1;}
elsif ($arg=~/^filterOutQueryNameHits=(.*)$/){ $par{filterOutQueryNameHits} = $1;}
elsif (-e $arg) { push(@fileIn,$arg); }
else {
die( "*** wrong command line arg '$arg'" );
}
}
$fileIn=$fileIn[0];
die ("missing input $fileIn") if (! -e $fileIn);
$alignTiling =1 if (! defined $alignTiling) ;
$maxAli =5000 if (! defined $maxAli) ;
$filterThre =100 if (! defined $filterThre) ;
$eThresh =100 if (! defined $eThresh ) ;
$short =0 if (! defined $short) ;
$#fileTmp=-1;
foreach $fileIn (@fileIn){
if ( $fileIn =~/\.list/ ) {
($Lok,$msg,$file,$tmp)=
&fileListRd($fileIn);if (! $Lok){ print "*** ERROR $scrName: input list\n",$msg,"\n";
exit; }
@tmpf=split(/,/,$file);
push(@fileTmp,@tmpf);
next;}
if ($fileIn !~ /\.list/) {push(@fileTmp,$fileIn);}
}
@fileIn= @fileTmp;
$#fileTmp=-1; # slim-is-in
foreach $fileIn (@fileIn){
++$ctfile;
if (! -e $fileIn){print "-*- WARN $scrName: no fileInBlast=$fileIn\n";
next;}
# output files
$id=$fileIn; $id=~s/^(.*\/)//; $dirIn=$1;
$id=~s/\..*$//;
$dirIn='' if (! defined $dirIn);
# BLAST output
if ($ctfile > 1 ){
$fileOutSaf=$id.$par{"extSaf"};
$fileInQuery=$dirIn.$id.$par{"extFasta"};
if ( $fileOutRdb ne '0' ) {$fileOutRdb=$id.$par{"extRdb"}; }
else{ $fileOutRdb=0; }
}
else {
if (! defined $fileOutSaf) {$fileOutSaf=$id.$par{"extSaf"};}
if (! defined $fileOutRdb) {$fileOutRdb="0"; }
elsif ($fileOutRdb eq "1") {$fileOutRdb=$id.$par{"extRdb"};}
if (! defined $fileInQuery) {$fileInQuery=$dirIn.$id.$par{"extFasta"}; }
}
if (! defined $fileInQuery) {
print "*** WARNING $scrName : query input file name is not defined\n";
}
($Lok,$msg)= &blastp_to_saf($fileIn,$fileInQuery,$fileOutSaf,$fileOutRdb,$filterThre,$maxAli,$alignTiling,$eThresh,$short);
if (! $Lok ) {
die( "*** ERROR blastpgp_to_saf.pl : '$msg'" );
}
elsif ($Lok == 2 ) {
warn( "*** WARNING blastpgp_to_saf.pl : '$msg'" );
}
}
#close FHERROR;
#unlink($fileErr) if (-z $fileErr);
exit(0);
#=============================================================================================
sub blastp_to_saf {
my ($Lok,$msg);
my $sbr="blastp_to_saf";
my ($blastfile,$queryfile,$fileout,$rdb,$filter,$maxAli,$tile,$eThresh,$short)=@_;
my (@query, %sequences,@alignedids,@namesSort,%rdb_lines);
my (@tmp_seq,@inserted_query,@seq,@alignedNames,%u_endings,%endings );
my ($key,$first,$last,$fhin,$local_counter,$beg,$index,$iter,$Score_count);
my ($Qflag,$fastaFlag);
local $queryLength;
$fhin= "FHIN";
#------------------- gets the query sequence and its length
undef @query; $fastaFlag='0';
# lkajan: this seems to confuse things when the name assigned here to queryName happens to be the same as one of the matches in the BLAST result
#$queryName = File::Basename::fileparse( $blastfile, qr/\.[^.]*$/o ); #$queryName.="_query";
$queryName = 'query';
if (-e $queryfile){
open($fhin,$queryfile) || confess("*** ERROR sbr: could not open $queryfile - no such file: $!");
#$queryName='query';
while(<$fhin>){
next if($_=~/^\n/ || $_=~/\// || $_=~/>/ || $_=~/#/ );
$_=~s/\s+//g;
@tmp=split(//o,$_);
push @query, @tmp;
}
close $fhin; $fastaFlag='1';
$queryLength=@query;
}
else { $fastaFlag='0';$queryName='query';}
#..........................................................
#if ( $rdb ne '0' && $rdb ne '' ){
#$rdbFile=$rdb;
#($Lok,$msg)= &printRdbHeader();
#if (! $Lok){ return(0,"*** ERROR $sbr : $msg"); }
#}
#------------------- finds number of iterations in blast file
open($fhin,$blastfile) || return(0,"*** ERROR $sbr: failed to open blast file $blastfile\n");
$iter=0; $nohits=0; $Qflag='closed';
while(<$fhin>){
if (! $fastaFlag){
if($_=~/^Query=/){$Qflag='open'; next;}
if( $_=~/letters\)/ && $Qflag eq 'open'){
$queryLength=$_; chomp $queryLength;
$queryLength=~s/^\s*\(([0-9]*)\s*letters.*$/$1/;
}
}
if($_=~/^Database:/){ $Qflag='closed';}
if($_=~/No hits found/){$nohits=1; last;}
if($_=~/^Searching../){
$iter++;
}
}
close $fhin;
if( ! defined $queryLength ) {return(0,"*** ERROR $sbr: failed to obtain length of query"); }
if ( $rdb ne '0' && $rdb ne '' ){
$rdbFile=$rdb;
($Lok,$msg)= &printRdbHeader();
if (! $Lok){ return(0,"*** ERROR $sbr : $msg"); }
}
if( ! $fastaFlag) { for ($i=0;$i<$queryLength;$i++){$query[$i]='.';} }
if ($nohits eq '1'){
$sequences{''}=''; @alignedNames=();
($Lok,$msg)=&print_saf_file($fileout,$queryName,$queryLength,\%sequences,\@alignedNames,@query);
return(0,"*** ERROR $sbr : $msg") if (! $Lok );
return(2,"*** WARNING $sbr : no hits found in Blastpgp search ");
}
return(0,"*** ERROR $sbr: blast file format not recognized") if ($iter == 0);
#............................................................
#--------------------------------skips to the last iteration
open($fhin,$blastfile) || return(0,"*** ERROR $sbr: failed to open blast file $blastfile\n");
$local_counter=0;
while(<$fhin>){
if($_=~/^Searching../){
$local_counter ++;
}
last if($local_counter == $iter);
}
#............................................................
undef @alignedNames; undef @alignedids; $Score_count=0; undef %multi_aligned; $global_count=0; undef %rdb_lines;
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
while(1)
{
# lkajan: processing of a record is done when the beginning of the /following/ record is reached.
# lkajan: the last record therefore is processed when we reach the end of the input file - we do not rely on the
# lkajan: Number of Hits line any more - this allows truncated blast input (some user in Yanay's lab has such)
my $bline = <$fhin>;
if( !$bline || $bline=~/^>/o )
{
if( $main::par{debug} ){ warn( "reading ".( $bline ? $bline : "undef" )); }
if($global_count > 0){
undef %u_endings;
undef @blastdat; @blastdat=@{ $rdb_lines{$id}{'1'} };
$bexp=$blastdat[$#blastdat-1];
if($bexp =~ /e/){ @tmp=split(/e/,$bexp);
if($tmp[0] eq ''){$tmp[0]=1;}
$bexp=$tmp[0] * 10**($tmp[1]);
}
my $includeFlag='yes';
if ($bexp > $eThresh) { $includeFlag='no'; if( $main::par{debug} ){ warn("exluding $id: $bexp > $eThresh"); } }
@seq=@{ $multi_aligned{1} };
if( ($includeFlag eq 'yes') && ($tile ne "0") && ($Score_count > 1) ){
$u_endings{1}[0]=$endings{1}[0]; $u_endings{1}[1]=$endings{1}[1];
$mflag=0;@store_rdb_lines=();
# lkajan: this loop handles the case where multiple HSPs are returned
foreach $itnum (2 .. $Score_count){
@temp=@{ $multi_aligned{$itnum} };
undef @blastdat; @blastdat=@ { $rdb_lines{$id}{$itnum} };
$bexp=$blastdat[$#blastdat-1];
if($bexp =~ /e/){ @tmp=split(/e/,$bexp);
if($tmp[0] eq ''){$tmp[0]=1;}
$bexp=$tmp[0] * 10**($tmp[1]);
}
if ($bexp > $eThresh) { delete $rdb_lines{$id}{$itnum}; if( $main::par{debug}){ warn("skipping $id:$itnum 'cause $bexp > $eThresh"); } next; }
$iffy=1;
# lkajan: This extends $u_endings{$it}[0..1] only in case $endings{$itnum}[0..1] entirely covers all $u_endings seen so far
foreach $it ( 1 .. ($itnum-1)){
if (defined $u_endings{$it}){
if ($endings{$itnum}[0] >= $u_endings{$it}[0] && $endings{$itnum}[0] <= $u_endings{$it}[1] ){ $iffy=0;last;}
if ($endings{$itnum}[1] >= $u_endings{$it}[0] && $endings{$itnum}[1] <= $u_endings{$it}[1] ){ $iffy=0;last;}
}
}
if ($iffy==1){
$u_endings{$itnum}[0]=$endings{$itnum}[0]; $u_endings{$itnum}[1]=$endings{$itnum}[1];
$one=$u_endings{$itnum}[0]; $two=$u_endings{$itnum}[1];
@seq[$one .. $two]=@temp[$one .. $two];
$mflag=1; push @store_rdb_lines, $itnum;
}
else{delete $rdb_lines{$id}{$itnum}; }
}
}
foreach $elem (@seq){
if(($elem ne ".") && ($elem !~ /[a-z_A-Z]/)){
$elem=".";
}
}
if( $main::par{debug} ){ warn("include $includeFlag id $id seq ".join('', @seq )); }
if ($includeFlag eq 'yes') { $sequences{$id}=[ @seq ]; }
else { $tmp=pop @alignedids; }
}
$global_count++;
undef @seq; $Score_count=0; undef %multi_aligned; undef %endings;
undef %u_endings;
#--- getting name of aligned sequence
for($it=0;$it<=$queryLength-1;$it++){ $seq[$it]="."; } #initialising array seq
if( $bline )
{
$bline=~s/^>//o;
$id=$bline; $id=~s/^(\S*)\s+(.*)\s*$/$1/o;
$protDspt=$2; chomp $protDspt;
push @alignedids, $id;
}
else { last; }
} #------------------------------------
if ($bline=~/^ Score/){
$Score_count++;
for($it=0;$it<=$queryLength-1;$it++){ $block_seq[$it]="."; }
undef @ali_para;
}
if ( $Score_count > 1 && $tile==0 ){ if( $main::par{debug} ){ warn("skipping $bline 'cause $Score_count > 1 && $tile==0"); } next; }
#-----------------------------------------------------------------------------------------------------
if ( 1 > 0){
if ( $bline=~ /\s+Length/){ $len2=$bline;$len2=~s/.+=\s*([0-9]+).*$/$1/;$len2=~s/\s//g;}
if ( $bline=~ /Score/ ){
$lali=$pid=$sim=$bitScore=$expect=''; $gap=0;
$line=$bline;
chomp $line; @tmp=split(/\,/,$line);
push @ali_para,@tmp;
}
if ( $bline=~ /Identities/){
$line=$bline; chomp $line;
@tmp=split(/\,/,$line); push @ali_para,@tmp;
foreach $param (@ali_para){
$param=~s/\s+//g;
if ($param=~/Score/){ $bitScore=$param; $bitScore=~s/^.+=(.+)bits.*$/$1/;}
elsif ($param=~/Expect/){@temp=split(/=/,$param); $expect=$temp[1];}
elsif ($param=~/Identities/){$lali=$param; $lali=~s/.+\/([0-9]+)\(([0-9]+)%\).*$/$1/;
$pid=$2;}
elsif ($param=~/Positives/){$sim=$param; $sim=~s/^.+\(([0-9]+)%\).*$/$1/;}
elsif ($param=~/Gaps/){$gap=$param; $gap=~s/^.+=([0-9]+)\/.*$/$1/;}
}
$lali=$lali-$gap;
$qLength=$queryLength;
$rdb_lines{$id}{$Score_count}=[$qLength,$len2,$lali,$pid,$sim,$gap,$bitScore,$expect,$protDspt];
}
}
#-----------------------------------------------------------------------------------------------------
# 0 1 2 3
# Query: 0 ---
# Query: 0
# Query: 85 AGAWRLLGVPGAAGPSGSSGSPGAAGASGSAGA 117
# Query: 118 PGAAGASGFPG-----------------------------------RPGAARASGAAGAS 142
# Query: 203 PLLVPEREVEDAARATSTEAFQPVYTREAAYA 234
if($bline=~/^Query:/){ @tmp=split(/\s+/o,$bline); undef @aligned; undef @inserted_query;
$beg=$tmp[1]-1; if( $beg == -1 ) { $end = -1; } else { $end=$tmp[3]-1; }
if( !defined( $endings{$Score_count}[0] ) || $endings{$Score_count}[0] < 0 ){ $endings{$Score_count}[0]=$beg;}
$endings{$Score_count}[1]=$end;
if( defined($tmp[2]) ){ @inserted_query=split(//o,$tmp[2]); }
}
if($bline=~/^Sbjct:/){
# Sbjct: 693 TGA 695
# Sbjct: 189 189
# Sbjct: 696 KGVRGMPGFPGASGEQGLKGFPGDPGREGFPGP 728
# Sbjct: 729 PGFMGPRGSKGTTGLPGPDGPPGPIGLPGPAGPPGDRGIPGEVLGAQPGTRGDAGLPGQP 788
# Sbjct: 848 LGQPGSPGLGGLPGDRGEPGDPGVPGPVGMKG 879
@tmp=split(/\s+/o,$bline);
@aligned=split(//o,$tmp[2]);
#getting rid of insertions at query sequence
cluck( " *** ERROR sbr: blastp_to_saf in lenghts for $id" ) if (@inserted_query != @aligned);
$local_counter=0;
undef @tmp_seq;
for($it=0;$it <= $#inserted_query; $it++){
if ($inserted_query[$it] =~ /[a-z_A-Z]/o){
if(! $fastaFlag){$query[$beg + $local_counter]=$inserted_query[$it];}
$tmp_seq[$local_counter]=$aligned[$it];
$local_counter++;
}
}
#@aligned=@tmp_seq; #-------------------------------------------
#+++++++++++=
if( $main::par{debug} ){ warn("seq after gap removal #$Score_count ".substr( $id, 0, 8 ).": ".join('', @tmp_seq )); }
if( $beg >= 0 )
{
@block_seq[$beg .. ($beg+$#tmp_seq)]=@tmp_seq; #----alignig part of the subject seguence
$multi_aligned{$Score_count}=[ @block_seq ];
}
}
}
close $fhin;
if( $main::par{debug} ){ warn("queryName: $queryName"); warn("alignedids: @alignedids"); }
#getting rid of repeats in the list
undef @namesSort;
push @namesSort, $queryName;
$Lname=$queryName; $Lname = lc($Lname);
if( $main::par{filterOutQueryNameHits} )
{
foreach $it (@alignedids){
$rflag=0; @tmp=split(/\|/o,$it);
if( $it eq $queryName || lc($it) eq $Lname ){ $rflag=1;}
else {
foreach $elem (@tmp){
if($elem eq $queryName || lc($elem) eq $Lname ){$rflag=1;}
}
}
if($rflag == 0){push @namesSort, $it;}
}
}
else { push @namesSort, @alignedids }
@alignedids=@namesSort[1 .. $#namesSort];
undef @namesSort;
{
my %namesSort = ( $queryName => 1 );
push @namesSort, $queryName;
# lkajan: the purpose of the following seem to be to remove duplicate identifiers from @alignedids. Now what about multiple HSPs for the same one sequence?
# lkajan: Why do we want to eliminate those? This does not seem right to me. However the 'logic' below seems to rely on the uniqueness of the members of
# lkajan: @alignedids so let's leave this code in place
foreach $it (@alignedids){
if( !$namesSort{$it} ){ push @namesSort, $it; } else { if( $main::par{debug} ){ cluck("duplicate identifier in blast output '$it' skipped"); } }
$namesSort{$it}++;
}
}
@alignedNames=@namesSort[1 .. $#namesSort];
if( $main::par{debug} ){ warn("namesSort: @namesSort"); warn("alignedNames: @alignedNames"); }
#-------------------------------------
#--filtering alignment
if($filter != 100){
($Lok,$msg)=&saf_filter(\@alignedNames,\%sequences,\@query,$filter,$maxAli);
return(0,"*** ERROR $sbr : $msg") if(! $Lok );
}
#----------------------------------- printing out the resulting files
if ($rdb ne '0' ){
foreach $id (@alignedNames){
foreach $score (sort keys %{ $rdb_lines{$id} }){
if($score > 1){ foreach $it ( @{ $rdb_lines{$id}{$score} }){$it='!'.$it;} }
($qLength,$len2,$lali,$pid,$sim,$gap,$bitScore,$expect,$protDspt)= @{ $rdb_lines{$id}{$score} };
#write FHRDB;
print FHRDB "$id\t$len2\t$pid\t$sim\t$lali\t$gap\t$bitScore\t$expect\t$protDspt\n";
}
}
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short naming format
if($short eq "1"){
undef @short_alignedNames; undef %tmp_sequences;
foreach $key (@alignedNames){
if($key =~ /trembl/ || $key =~/swiss/ || $key=~/pdb/){
@tmp=split(/\|/,$key); $short=$tmp[2];
}
else { $short=$key;}
push @short_alignedNames, $short;
}
@alignedNames=@short_alignedNames;
foreach $key (keys %sequences){
if($key =~ /trembl/ || $key =~/swiss/ || $key =~/pdb/){
@tmp=split(/\|/,$key);
$temp=$tmp[$#tmp];
$tmp_sequences{$temp}=$sequences{$key};
}
else { $tmp_sequences{$key}=$sequences{$key}; }
}
%sequences=%tmp_sequences;
}
if( $par{debug} )
{
foreach $key (@alignedNames)
{
warn( "alignedName: $key\n".join('', @{$sequences{$key}} ) );
}
}
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
($Lok,$msg)=&print_saf_file($fileout,$queryName,$queryLength,\%sequences,\@alignedNames,@query);
return (0,"*** ERROR $sbr : $msg") if ( ! $Lok );
return (2,"*** WARNIG $sbr : no hits found after filtering for $queryName") if ( $#alignedNames < 0);
if (-e $fileout) { return (1,"ok"); }
else { return (0,"*** ERROR $sbr : failed to produce the saf output file"); }
} # end of blastp_to_saf
#==============================================================================
sub saf_filter{
my $sbr='saf_filter';
my ($Lok,$msg);
local($array_name,$ali_hash,$query,$red,$bound)=@_;
my @ord_ali_list=@$array_name;
my %alignment=%$ali_hash;
my @queryLoc=@$query;
my @new_aligned_names=();
my ($count,$ct,$same);
@last= @queryLoc;
$len=$#last;
$count=0;
Floop:for($index=0; $index <= $#ord_ali_list; $index++){
if ( ! defined $alignment{$ord_ali_list[$index]}) { return(0,"*** ERROR $sbr : alignment to be filtered is not defined\n")}
@maybe=@{ $alignment{$ord_ali_list[$index]} };
$ct=$same=0;
foreach $itres (0..$len) {
next if ($maybe[$itres] !~ /[a-z_A-Z]/);
next if ( $last[$itres] !~ /[a-z_A-Z]/);
++$same if ($maybe[$itres] eq $last[$itres]);
++ $ct;
}
if ( ( $ct > 0 && (100*$same/$ct) < $red ) || $ct==0 ){
@last=@maybe; $count++;
push @new_aligned_names, $ord_ali_list[$index];
last Floop if ($count >= $bound);
}
}
@$array_name=@new_aligned_names;
return(1,"filtering is done");
}
#==============================================================================================
#==============================================================================================
sub printRdbHeader{
my $sbr='printRdbHeader';
my ($Lok,$msg);
#a report on blastpgp file
$header="# PERL-RDB"."\n";
$header.="# SEQLENGTH\t $queryLength"."\n";
$header.="# ID\t:\tidentifier of the aligned (homologous) protein"."\n";
$header.="# LSEQ2\t:\length of the entire sequence of the aligned protein"."\n";
$header.="# LALI\t:\tlength of the alignment excluding insertions and deletions"."\n";
$header.="# %IDE\t:\tpercent indentity"."\n";
$header.="# %SIM\t:\tpercent similarity"."\n";
$header.="# LGAP\t:\ttotal gap length"."\n";
$header.="# BSCORE\t:\tblast score (bits)"."\n";
$header.="# BEXPECT\t:\tblast expectation value"."\n";
$header.="# PROTEIN\t:\tone-line description of aligned protein"."\n";
$header.="# '!'\t:\tindicates adjacent blast alignment combined with the previous one"."\n";
$header.="# ID\tLSEQ2\t%IDE\t%SIM\tLALI\tLGAP\tBSCORE\tBEXPECT\tPROTEIN\n";
open(FHRDB,">$rdbFile") || return(0, "*** ERROR $sbr : could not open rdbfile=$rdbFile for writing\n");
print FHRDB $header;
return( 1,'ok');
}
#==============================================================================================
#==============================================================================================
sub print_saf_file{
my $sbr='print_saf_file';
my ($Lok,$msg);
local($fileout,$queryName,$queryLength,$alignment,$aliNames,@query)=@_;
my %sequences=%$alignment;
my @alignedNames=@$aliNames;
my ($fhout,$pages,$nameField);
#foreach $key (@alignedNames){
#print $key."\n";
#print @{ $sequences{$key} },"\n";
#}
#exit;
$fhout="FHOUT";
$pages=int $queryLength/50;
if ($queryLength%50 != 0){$pages++;}
open($fhout,">$fileout") || return(0,"*** ERROR $sbr: failed to open fileout=$fileout for writing");
print $fhout "# SAF (Simple Alignment Format)\n";
print $fhout "#\n";
$nameField=0;
@tmp=split(//,$queryName);
if ($#tmp+2>$nameField){$nameField=$#tmp+2;}
foreach $key (@alignedNames){
@tmp=split(//,$key);
if ($#tmp+2>$nameField){$nameField=$#tmp+2;}
}
for($it=1;$it<=$pages;$it++){
$beg=($it-1)*50; $end=$it*50-1;
printf $fhout "%-${nameField}.${nameField}s", $queryName;
for($index=0;$index<50;$index=$index+10){
$first=$beg+$index; $last=$first+9;
#print "@query\n",$query[$first]," $query[$last]\n";
if ($last <= $queryLength -1 ){print $fhout @query[$first .. $last]," " ;}
else { print $fhout @query[$first .. ($queryLength-1)]; }
}
print $fhout "\n";
foreach $key (@alignedNames){
printf $fhout "%-${nameField}.${nameField}s", $key;
for($index=0;$index<50;$index=$index+10){
$first=$beg+$index; $last=$first+9;
if ($last <= $queryLength -1 ){
print $fhout @{ $sequences{$key}}[$first .. $last]," " ;
}
else { print $fhout @{ $sequences{$key}}[$first .. ($queryLength-1)]," " ; }
}
print $fhout "\n";
}
print $fhout "\n";
}
close $fhout;
return (1,'ok');
}
#======================================================================
sub helpLocal {
#-------------------------------------------------------------------------------
# helpLocal
#-------------------------------------------------------------------------------
if ($#ARGV<0 || # help
$ARGV[0] =~/^(-h|help|special)/){
print "goal: $scrGoal\n";
print "use: $scrName file_blastpgp fasta=(file_fasta) \n \n";
print " will convert without file_fasta specified \n";
print " but in some cases you may loose part of query \n";
print " submitted to blastpgp \n";
print "opt: \n";
# 'keyword' 'value' 'description'
printf "%5s %-15s=%-20s %-s\n","","saf", "x", "name of saf output file; if not specified";
printf "%5s %-15s %-20s %-s\n","","", "", "default 'saf' extension used";
printf "%5s %-15s=%-20s %-s\n","","rdb", "x", "either just 'rdb' -> will write blastRdb file";
printf "%5s %-15s %-20s %-s\n","","", "", "or full name of blastRdb file";
printf "%5s %-15s=%-20s %-s\n","","red", "x", "value for filtering saf file (def=100)";
printf "%5s %-15s=%-20s %-s\n","","maxAli", "x", "maximum number of aligned sequnces";
printf "%5s %-15s %-20s %-s\n","","", "", "after filtering (def: 1500)";
printf "%5s %-15s=%-20s %-s\n","","tile", "x", "either just 'tile' -> will tile blast prediction in saf";
printf "%5s %-15s %-20s %-s\n","","", "", "or 'tile=(0|1)' to enable|disable tiling (def 1)";
printf "%5s %-15s=%-20s %-s\n","","eSaf", "x", "maximum blast expect value to be included in 'saf' file";
printf "%5s %-15s=%-20s %-s\n","","short", "x", "will write short id's in the in the saf output file \n";
printf "%5s %-15s=%-20s %-s\n","","extSaf", "x", "specify an extension for the saf file(useful for list processing";
printf "%5s %-15s=%-20s %-s\n","","extFasta", "x", "specify an extension for the fasta file(useful for list processing";
printf "%5s %-15s=%-20s %-s\n","","extRdb", "x", "specify an extension for the rdb file(useful for list processing";
printf "%5s %-15s=%-20s %-s\n","","debug", "x", "debugging messages [0*|1]";
printf "%5s %-15s=%-20s %-s\n","","filterOutQueryNameHits", "x", "filter out hits with the same name as query [0*|1]";
exit;
}
} # end of helpLocal
#===============================================================================
sub fileListRd {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
#-------------------------------------------------------------------------------
# fileListRd reads a list of files
# in: file_list= file with filenames
# in: $fhErrSbr= file handle to report missing files
# (0 to surpress warnings!)
# in: $extForChain= 'ext1,ext2' : extensions to check for chains,
# i.e. if not existing purge ext_[A-Z0-9]
# in: $dirLoc= 'dir1,dir2' : directories to scan for file
# out: 1|0,msg
# out: $list= 'file1,file2,...'
# out: $chain= 'c1,c2,...' : if chains found
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."fileListRd";$fhinLoc="FHIN_fileListRd";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
#$fhErrSbr="STDOUT" if (! defined $fhErrSbr);
$extForChain=0 if (! defined $extForChain);
return(0,"*** $sbrName: miss in file '$fileInLoc'!",0) if (! -e $fileInLoc);
@extLoc=split(/,/,$extForChain) if ($extForChain);
@dirLoc=split(/,/,$dirLoc) if ($dirLoc);
# ------------------------------
# open file
open($fhinLoc,$fileInLoc) ||
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n",0);
$tmpChain=$tmpFile=""; # ------------------------------
while (<$fhinLoc>) { # read list
$_=~s/\n|\s//g; $file=$_;
next if (length($_)==0);
if (-e $file) {
$tmpFile.="$file,";$tmpChain.="*,";} # file ok
else {$Lok=0;$chainTmp="unk";
foreach $ext (@extLoc){ # check chain
foreach $dir ("",@dirLoc){ # check dir (first: local!)
$fileTmp=$file; $dir.="/" if (length($dir)>0 && $dir !~/\/$/);
$fileTmp=~s/^(.*$ext)\_([A-Z0-9])$/$1/;
$chainTmp=$2 if (defined $2);
$fileTmp=$dir.$fileTmp;
$Lok=1 if (-e $fileTmp);
last if $Lok;}
last if $Lok;}
if ($Lok){$tmpFile.="$fileTmp,";
$tmpChain.="*," if (! defined $chainTmp || $chainTmp eq "unk");
$tmpChain.="$chainTmp," if (defined $chainTmp && $chainTmp ne "unk"); }
else { print "-*- WARN $sbrName missing file=$_,\n";}}
}close($fhinLoc);
$tmpFile=~s/^,*|,*$//g;$tmpChain=~s/^,*|,*$//g;
return(1,"ok $sbrName",$tmpFile,$tmpChain);
} # end of fileListRd
#==================================================================================
# vim:ai:
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