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blast2xml.pl
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blast2xml.pl
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use Carp;
use English;
use File::Basename;
use Getopt::Long;
use Data::Dumper;
#use Devel::Size qw(size total_size);
use strict;
use warnings;
#use IO qw(Handle File);
#use XML::Writer;
### Blast 2 xml parser
# 1. read results from UBlast
# Format is userdefined:
#
my $verbose = 0;
my $blast_output_file = "blast.out";
my $blast_xmloutput_file = "blast_out.xml";
my $options = GetOptions ("in|i=s" => \$blast_output_file, # numeric
"out|o=s" => \$blast_xmloutput_file, # string
"verbose" => \$verbose);
#('in|i=s' => \$blast_output_file,
# 'out|o=s' => \$blast_xmloutput_file,
# );
if(! -e $blast_output_file|| ! -s $blast_output_file){
print "Could not find Blast output file. Exiting\n";
exit;
}
my $print_alignment = 1;
my %statistics_hash;
#my @statistics_array;
my $noOfQuery = 0;
my %seq_length_hash = ();
my %seen_hash = ();
my $previous_target_name;
my $previous_query_name;
my @hit_object;
my %duplicate_entries_hash = ();
my $count_query_hits = 1;
my $hit_counter = 1;
my $lastHit = 0;
my @statistics_array;
my $hsp_no = -1;
#print "Reading from $blast_output_file\n";
# print XML start
#&write_xml_start();
print "<BlastOutput>\n";
open my $blast_output_FH, '<', $blast_output_file or croak "Couldn't open '$blast_output_file': ";
my $firstLine = <$blast_output_FH>;
while (<$blast_output_FH>) {
#while (my $line = <$blast_output_FH>) {
chomp();
my $line = $_;
#print "\tline is $line\n";
#next if /^\s*#/;
#next if !(/\w+/);
next if /^query/;
my @splitted_line = split;
my @hsp_array;
if(!scalar(@splitted_line) == 11){
print "\tError parsing line $line: has too few entries (should be 11)";
print "$line\n";
exit;
}
# query and target
my ($query_name, $target_name,
$bit_score, $query_length,
$hit_length, $query_start,
$query_end, $hit_start,
$hit_end,$query_ali_length,$hit_ali_length
) = (@splitted_line);
if(!defined($query_name) || !defined($target_name) || !defined($bit_score) || !defined($query_length) || !defined($hit_length) || !defined($query_start)
|| !defined($query_end) || !defined($hit_start) || !defined($hit_end) || !defined($query_ali_length) || !defined($hit_ali_length) ){
print "\tproblem parsing line $line\n";
#print "queryName: $query_name\n, targetName: $target_name,
# bitScore: $bit_score, QueryLength: $query_length,
# hitLength: $hit_length, QueryStart: $query_start,
# QueryEnd: $query_end, HitStart: $hit_start,
# HitEnd: $hit_end, QueryAliLength: $query_ali_length, HitAliLength: $hit_ali_length\n";
#exit;
next;
}
$previous_target_name = $target_name if !defined($previous_target_name);
$previous_query_name = $query_name if !defined($previous_query_name);
# write entry
if($target_name ne $previous_target_name){
#print Dumper @statistics_array;
#exit;
my $hspCounter = 0;
next if $previous_query_name =~ /query_length/;
my $output_string = q{};
#my $writer = new XML::Writer( OUTPUT => \$output_string, DATA_MODE => 1, DATA_INDENT => 1 );
#&write_query_start($writer,$count_query_hits,$previous_query_name, $seq_length_hash{$previous_query_name});
print "\t<Iteration>\n";
print "\t <Iteration_iter-num>$count_query_hits</Iteration_iter-num>\n";
print "\t <Iteration_query-def>$previous_query_name</Iteration_query-def>\n";
print "\t <Iteration_query-len>$seq_length_hash{$previous_query_name}</Iteration_query-len>\n";
# Hit
#$writer->startTag( 'Iteration_hits' );
print "\t <Iteration_hits>\n";
#&write_hit_start($writer,$hit_counter,$previous_target_name, $seq_length_hash{$previous_target_name});
print "\t <Hit>\n";
print "\t <Hit_num>$hit_counter</Hit_num>\n";
print "\t <Hit_id>$previous_target_name</Hit_id>\n";
print "\t <Hit_def>$previous_target_name</Hit_def>\n";
print "\t <Hit_len>$seq_length_hash{$previous_target_name}</Hit_len>\n";
print "\t <Hit_hsps>\n";
# Hsp
#print "unequal\n";
foreach (@statistics_array){
my @hsp_array = $_;
my ($bit_score, $query_length, $hit_length, $query_start, $query_end, $hit_start, $hit_end, $query_ali_length, $hit_ali_length
) = ($hsp_array[0][0],$hsp_array[0][1],$hsp_array[0][2],$hsp_array[0][3],$hsp_array[0][4],$hsp_array[0][5],$hsp_array[0][6],$hsp_array[0][7],$hsp_array[0][8]);
if(!defined($bit_score) || !defined($query_length) || !defined($hit_length) || !defined($query_start)
|| !defined($query_end) || !defined($hit_start) || !defined($hit_end) || !defined($query_ali_length) || !defined($hit_ali_length) ){
print "\tproblem parsing line $line\n";
#print "queryName: $query_name\n, targetName: $target_name,
# bitScore: $bit_score, QueryLength: $query_length,
# hitLength: $hit_length, QueryStart: $query_start,
# QueryEnd: $query_end, HitStart: $hit_start,
# HitEnd: $hit_end, QueryAliLength: $query_ali_length, HitAliLength: $hit_ali_length\n";
#exit;
next;
}
$hspCounter++;
print "\t <Hsp>\n";
print "\t <Hsp_num>$hspCounter</Hsp_num>\n";
print "\t <Hsp_bit-score>$bit_score</Hsp_bit-score>\n";
print "\t <Hsp_query-from>$query_start</Hsp_query-from>\n";
print "\t <Hsp_query-to>$query_end</Hsp_query-to>\n";
print "\t <Hsp_hit-from>$hit_start</Hsp_hit-from>\n";
print "\t <Hsp_hit-to>$hit_end</Hsp_hit-to>\n";
print "\t <Hsp_align-len>$hit_ali_length</Hsp_align-len>\n";
if($print_alignment){
print "\t <Hsp_qseq>A</Hsp_qseq>\n";
print "\t <Hsp_hseq>A</Hsp_hseq>\n";
}
print "\t </Hsp>\n";
#print "write hsp with $hspCounter, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length\n";
#&write_hsp($writer, $hspCounter, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length);
}
#Finish hit
#$writer->endTag( 'Hit_hsps' );
#$writer->endTag( 'Hit' );
print "\t </Hit_hsps>\n";
print "\t </Hit>\n";
#&write_hit_end($writer);
#Finish query
print " </Iteration_hits>\n";
print " </Iteration>\n";
#&write_query_end($writer);
# #Finish xml
#print $output_string;
#last if $count_query_hits == 1;
$count_query_hits++;
@statistics_array = ();
$hsp_no = 0;
#print "\tclean statistics array\n";
}
else{
$hsp_no++;
}
$previous_target_name = $target_name;
$previous_query_name = $query_name;
#Avoid duplicate entries:
if($duplicate_entries_hash{$line}){
#print "duplicate line\n";
next;
}
$duplicate_entries_hash{$line} = 1;
# query+target+bits+ql+tl+qlo+qhi+tlo+thi+qs+ts+qrow+trow
# Sequence lenght of query and hit
$seq_length_hash{$query_name} = $splitted_line[3];
$seq_length_hash{$target_name} = $splitted_line[4];
###
# 0 -bit_score
# 1 - query_length
# 2 - hit_length
# 3 - query_start
# 4 - query_end
# 5 - hit_start
# 6 - hit_end
# 7 - query_ali_length
# 8 - hit_ali_length
#print "\thsp no: $hsp_no\n";
#print "\thsp no: $hsp_no\n";
#push @{ $AoA[0] }, "wilma", "betty";
$statistics_array[$hsp_no][0] = $bit_score;
#print "$statistics_array[$hsp_no][0]\n";
$statistics_array[$hsp_no][1] = $query_length;
$statistics_array[$hsp_no][2] = $hit_length;
$statistics_array[$hsp_no][3] = $query_start;
$statistics_array[$hsp_no][4] = $query_end;
$statistics_array[$hsp_no][5] = $hit_start;
$statistics_array[$hsp_no][6] = $hit_end;
$statistics_array[$hsp_no][7] = $query_ali_length;
$statistics_array[$hsp_no][8] = $hit_ali_length;
}
close $blast_output_FH or croak "Couldn't close '$blast_output_file': ";
#&write_xml_end();
#exit;
my $output_string;
my $hspCounter = 0;
#print "forgot the last hit\n";
#print Dumper @statistics_array;
#my $writer = new XML::Writer( OUTPUT => \$output_string, DATA_MODE => 1, DATA_INDENT => 1 );
print "\t<Iteration>\n";
print "\t <Iteration_iter-num>$count_query_hits</Iteration_iter-num>\n";
print "\t <Iteration_query-def>$previous_query_name</Iteration_query-def>\n";
print "\t <Iteration_query-len>$seq_length_hash{$previous_query_name}</Iteration_query-len>\n";
print "\t <Iteration_hits>\n";
#&write_hit_start($writer,$hit_counter,$previous_target_name, $seq_length_hash{$previous_target_name});
print "\t <Hit>\n";
print "\t <Hit_num>$hit_counter</Hit_num>\n";
print "\t <Hit_id>$previous_target_name</Hit_id>\n";
print "\t <Hit_def>$previous_target_name</Hit_def>\n";
print "\t <Hit_len>$seq_length_hash{$previous_target_name}</Hit_len>\n";
print "\t <Hit_hsps>\n";
#&write_query_start($writer,$count_query_hits,$previous_query_name, $seq_length_hash{$previous_query_name});
#&write_hit_start($writer,$hit_counter,$previous_target_name, $seq_length_hash{$previous_target_name});
foreach (@statistics_array){
my @hsp_array = $_;
#print Dumper @hsp_array;
#exit;
my ($bit_score, $query_length, $hit_length, $query_start, $query_end, $hit_start, $hit_end, $query_ali_length, $hit_ali_length
) = ($hsp_array[0][0],$hsp_array[0][1],$hsp_array[0][2],$hsp_array[0][3],$hsp_array[0][4],$hsp_array[0][5],$hsp_array[0][6],$hsp_array[0][7],$hsp_array[0][8]);
$hspCounter++;
#$hsp, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length
#print "write hsp with $hspCounter, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length\n";
#next;
print "\t <Hsp>\n";
print "\t <Hsp_num>$hspCounter</Hsp_num>\n";
print "\t <Hsp_bit-score>$bit_score</Hsp_bit-score>\n";
print "\t <Hsp_query-from>$query_start</Hsp_query-from>\n";
print "\t <Hsp_query-to>$query_end</Hsp_query-to>\n";
print "\t <Hsp_hit-from>$hit_start</Hsp_hit-from>\n";
print "\t <Hsp_hit-to>$hit_end</Hsp_hit-to>\n";
print "\t <Hsp_align-len>$hit_ali_length</Hsp_align-len>\n";
if($print_alignment){
print "\t <Hsp_qseq>A</Hsp_qseq>\n";
print "\t <Hsp_hseq>A</Hsp_hseq>\n";
}
print "\t </Hsp>\n";
#&write_hsp($writer, $hspCounter, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length);
}
#Finish hit
print "\t </Hit_hsps>\n";
print "\t </Hit>\n";
#&write_hit_end($writer);
#Finish query
print " </Iteration_hits>\n";
print " </Iteration>\n";
#&write_query_end($writer);
# #Finish xml
#print $output_string;
print "\n</BlastOutput>\n";
exit;
&write_xml_end();
exit;
print "\thwaaaat?\n";
my $total_size = int(total_size(\%statistics_hash) / 1048576);
print "\tthe hash to keep all values used ".$total_size." Mbytes\n";
print "\tfinished the program successfully\n";
exit;
my $print_counter = 0;
#print "Writing file\n";
my $last_hit = q{};
sub write_xml_start {
# my $writer = shift;
print "<BlastOutput>\n";
# print "xml_start\n";
# $writer->xmlDecl( 'UTF-8' );
# $writer->doctype( 'BlastOutput' );
# $writer->startTag( 'BlastOutput' );
## HEADER
# $writer->dataElement( 'BlastOutput_program', "blastp" );
# $writer->dataElement( "BlastOutput_version", "blastp 2.2.22 [Sep-27-2009]" );
# $writer->dataElement( "BlastOutput_reference", "Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs;, Nucleic Acids Res. 25:3389-3402." );
# $writer->dataElement( "BlastOutput_db", "query" );
# $writer->dataElement( "BlastOutput_query", "blastp" );
# $writer->dataElement( "BlastOutput_query-ID", "lcl|1_0" );
# $writer->dataElement( "BlastOutput_query-def", "first_hit" );
# $writer->dataElement( "BlastOutput_query-len", "500" );
# $writer->startTag( 'BlastOutput_param' );
# Parameters
# $writer->startTag( 'Parameters' );
# $writer->dataElement( "Parameters_matrix", "BLOSUM62" );
# $writer->dataElement( "Parameters_expect", "blastp" );
# $writer->dataElement( "Parameters_gap-open", "11" );
# $writer->dataElement( "Parameters_gap-extend", "1" );
# $writer->dataElement( "Parameters_filter", "F" );
# $writer->endTag( 'Parameters' );
# $writer->endTag( 'BlastOutput_param' );
# $writer->startTag( 'BlastOutput_iterations' );
}
sub write_xml_end {
print "\n</BlastOutput>\n";
# my $writer = shift;
# my $output = shift;
# print "xml_end\n";
# $writer->endTag( 'BlastOutput_iterations' );
# $writer->endTag( 'BlastOutput' );
# $writer->end();
# $output->close();
}
sub write_hit_start {
my ($writer, $hit_counter,$hit, $seq_length) = (shift,shift,shift,shift);
$writer->startTag( 'Hit' );
$writer->dataElement( "Hit_num", "$hit_counter" );
$writer->dataElement( "Hit_id", $hit);
$writer->dataElement( "Hit_def", $hit);
$writer->dataElement( "Hit_accession", "0" );
$writer->dataElement( "Hit_len", $seq_length);
# Hsp
$writer->startTag( 'Hit_hsps' );
}
sub write_hit_end {
my $writer = shift;
$writer->endTag( 'Hit_hsps' );
$writer->endTag( 'Hit' );
}
sub write_query_start {
my ($writer, $count_query_hits,$query, $seq_length) = (shift,shift,shift,shift);
# print "query_start\n";
$writer->startTag( 'Iteration' );
# Iteration
$writer->dataElement( "Iteration_iter-num", "$count_query_hits" );
$writer->dataElement( "Iteration_query-ID", "lcl|1_0" );
$writer->dataElement( "Iteration_query-def", $query );
$writer->dataElement( "Iteration_query-len", $seq_length);
# Hit
$writer->startTag( 'Iteration_hits' );
}
sub write_query_end {
my $writer = shift;
# print "query_end\n";
$writer->endTag( 'Iteration_hits' );
$writer->startTag( 'Iteration_stat' );
$writer->startTag( 'Statistics' );
#$writer->dataElement( "Statistics_db-num", "3" );
#$writer->dataElement( "Statistics_db-len", "1777" );
#$writer->dataElement( "Statistics_hsp-len", "0" );
#$writer->dataElement( "Statistics_eff-space", "0" );
#$writer->dataElement( "Statistics_kappa", "0.041" );
#$writer->dataElement( "Statistics_lambda", "0.267" );
#$writer->dataElement( "Statistics_entropy", "0.14" );
$writer->endTag( 'Statistics' );
$writer->endTag( 'Iteration_stat' );
$writer->endTag( 'Iteration' );
}
sub write_hsp{
my ($writer, $hsp, $bit_score, $query_start, $query_end, $hit_start, $hit_end, $hit_ali_length) = @_;
$writer->startTag( 'Hsp' );
$writer->dataElement( "Hsp_num", $hsp );
$writer->dataElement( "Hsp_bit-score", $bit_score );
#$writer->dataElement( "Hsp_score", "0" );
#$writer->dataElement( "Hsp_evalue", "0" );
$writer->dataElement( "Hsp_query-from", $query_start );
$writer->dataElement( "Hsp_query-to", $query_end );
$writer->dataElement( "Hsp_hit-from", $hit_start );
$writer->dataElement( "Hsp_hit-to", $hit_end );
#$writer->dataElement( "Hsp_query-frame", "1" );
#$writer->dataElement( "Hsp_hit-frame", "1" );
#$writer->dataElement( "Hsp_identity", "0" );
#$writer->dataElement( "Hsp_positive", "0" );
#$writer->dataElement( "Hsp_gaps", "0" );
$writer->dataElement( "Hsp_align-len", $hit_ali_length );
## Alignments
if($print_alignment){
# $writer->dataElement( "Hsp_qseq", $statistics_hash{$query}{$hit}{$hsp}{'query_ali'} );
# $writer->dataElement( "Hsp_hseq", $statistics_hash{$query}{$hit}{$hsp}{'hit_ali'} );
$writer->dataElement( "Hsp_qseq", "A" );
$writer->dataElement( "Hsp_hseq", "A" );
}
# $writer->dataElement( "Hsp_midline", $statistics_hash{$query}{$hit}{'hit_end'} );
$writer->endTag( 'Hsp' );
}
1;