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HMMsearchOutput.pir
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#
# Output from HMMER.
#
- PerlClass PirObject::HMMsearchOutput
- InheritsFrom PirObject
- FieldsTable
# Field name Struct Type Comments
#---------------------- --------------- --------------- -----------------------
Iterations array <HMMIteration> Array of iterations can be used for hmmsearch or jackhmmer
- EndFieldsTable
- Methods
our $RCS_VERSION='$Id: HMMsearchOutput.pir,v 1.7 2011/03/31 19:43:47 nbeck Exp $';
our ($VERSION) = ($RCS_VERSION =~ m#,v ([\w\.]+)#);
sub FillFeaturesFromTextOutput {
my $self = shift;
my $tab = shift;
my $resume = ();
my @hitinfo = ();
my %hitinfo = ();
my $isRes = 0;
my $isAli = 0;
my $isStat = 0;
my $Iteration = new PirObject::HMMIteration();
my $Iterations = [];
my $Resumes = [];
my $HMMalis = [];
my $Alignments_a = [];
my $ali_lines = [];
my $Alignments_h = {};
my $BeforeThresh = 1;
my $NbResUpperTresh = 0;
foreach my $line(@$tab) {
$isRes = 1 if $line =~ /^Scores for complete sequences/o;
$BeforeThresh = 1 if $line =~ /^Scores for complete sequences/o;
next if $line =~ /^Scores for complete sequences/o;
if ($isRes == 1 ) {
$isRes = 0 if $line =~ /^\s+$/;
$BeforeThresh = 0 if ($line =~ m/------\s+inclusion\s+threshold\s+------/);
next if $line =~ m/Sequence\s+Description/ || $line =~ m/^\s*---/ || $line =~ /^\s*$/;
$line =~ s/^\+//;
$line =~ s/^\s+//;
my @info = split(/\s+/,$line);
my ($f_evalue,$f_score,$f_bias,$b_evalue,$b_score,$b_bias,$exp,$n,$name)
= ($info[0],$info[1],$info[2],$info[3],$info[4],$info[5],$info[6],$info[7],$info[8]);
my $len_info = scalar(@info) - 1;
my $desc = join( ' ', @info[9..$len_info] );
# Create Resume
my $Resume = new PirObject::HMMResume();
$Resume->set_fEvalue($f_evalue);
$Resume->set_fScore($f_score);
$Resume->set_fBias($f_bias);
$Resume->set_bEvalue($b_evalue);
$Resume->set_bScore($b_score);
$Resume->set_bBias($b_bias);
$Resume->set_exp($exp);
$Resume->set_NumAli($n);
$Resume->set_SequenceId($name);
$Resume->set_SeqIdAndDesc("$name $desc");
$Resume->set_Description($desc);
$Resume->set_BeforeThresh($BeforeThresh);
$NbResUpperTresh++ if $BeforeThresh == 1;
push(@$Resumes,$Resume);
push @hitinfo, [ $name, $desc, $f_evalue, $f_score ];
$hitinfo{$name} = $#hitinfo;
}
$isAli = 1 if $line =~ m/^Domain\s+annotation\s+for/;
next if $line =~ m/^Domain\s+annotation\s+for/;
if ($isAli) {
$isAli = 0 if $line =~ m/^Internal\s+pipeline\s+statistics\s+summary/;
next if $line =~ m/acc$/ || $line =~ m/^\s*---/;
push(@$ali_lines,$line);
if ($line =~ m/^>>/) {
$line =~ s/^>>\s+//;
my @info = split(/\s+/, $line);
my $ali_name = $info[0];
my $len_info = scalar(@info) - 1;
my $ali_desc = join( ' ', @info[1..$len_info]);
next;
}
if ($line =~ m/\s+\d+\s+[!|?]/) {
$line =~ s/^\s+//;
my @info = split(/\s+/,$line);
my ($d_num,$d_indic,$d_score,$d_bias,$d_cvalue,$d_ivalue,$d_hmmfrom,$d_hmmto,
$d_hmmbra,$d_alifrom,$d_alito,$d_alibra,$d_envfrom,$d_envto,$d_envbra,$d_acc) = @info;
my $HMMAli = new PirObject::HMMAli();
}
}
$isStat = 1 if ($line =~ m/^Internal\s+pipeline\s+statistics\s+summary/);
next if ($line =~ m/^Internal\s+pipeline\s+statistics\s+summary/);
if ($isStat == 1) {
next if $line =~ m/^\s*---/;
if ($line =~ m/^Query\s+model\(s\):\s+(.+)/) {
$Iteration->set_QueryModel($1);
$Iteration->set_ModelSize($1) if $Iteration->get_QueryModel() =~ m/\(\s*(\d+).+\)/;
}
$Iteration->set_TargetSequences($1) if $line =~ m/^Target\s+sequences:\s+(.+)/;
$Iteration->set_MSVFilter($1) if $line =~ m/^Passed\s+MSV\s+filter:\s+(.+)/;
$Iteration->set_BiasFilter($1) if $line =~ m/^Passed\s+bias\s+filter:\s+(.+)/;
$Iteration->set_VitFilter($1) if $line =~ m/^Passed\s+Vit\+filter:\s+(.+)/;
$Iteration->set_FwdFilter($1) if $line =~ m/^Passed\s+Fwd\+filter:\s+(.+)/;
$Iteration->set_SearchSpace($1) if $line =~ m/^Initial\s+search\s+space\s+\(Z\):\s+(.+)/;
$Iteration->set_domZ($1) if $line =~ m/^Domain\s+search\s+space\s+\(domZ\):\s+(.+)/;
$Iteration->set_CPUTime($1) if $line =~ m/^\#\s+CPU\s+time:\s+(.+)/;
$Iteration->set_McSec($1) if $line =~ m/^\#\s+Mc\/sec:\s+(.+)/;
$Iteration->set_NbResUpperTresh($NbResUpperTresh);
if ($line =~ m/^\#\s+Mc\/sec:\s+(.+)/){
my $all_alignments = &TreatAlignment($ali_lines);
&AddAliToResume($all_alignments,$Resumes);
$Iteration->set_resume($Resumes);
$Resumes = [];
$ali_lines = [];
push(@$Iterations,$Iteration);
$Iteration = new PirObject::HMMIteration();
}
$Iteration->set_IncludedMSA($1) if $line =~ m/^\@\@\s+New\s+targets\s+included:\s+(.+)/;
}
}
$self->set_Iterations($Iterations);
}
sub TreatAlignment {
my $lines = shift;
my ($name,$desc,$num_dom) = ("","","");
my $all_alignments = {};
my $alignments = {};
foreach my $line (@$lines){
next if $line =~ m/^\s$/ || $line =~ m/\s+Alignments\s+for/;
last if ($line =~ m/^\s+\[No\s+targets\s+detected\s+that\s+satisfy/);
if ($line =~ s/^>>\s+// || $line =~ m/^Internal\s+pipeline\s+statistics/) {
if ($name ne "") {
$all_alignments->{"$name $desc"} = $alignments;
$alignments = {};
}
my @info = split(/\s+/, $line);
$name = $info[0];
my $len_info = scalar(@info) - 1;
$desc = join( ' ', @info[1..$len_info]);
}
elsif ($line =~ m/^\s+\[No\s+individual\s+domains\s+that\s+satisfy/) {
my $HMMAli = new PirObject::HMMAli();
}
elsif ($line =~ m/\s+\d+\s+([!|?])/) {
$line =~ s/^\s+//;
my @info = split(/\s+/,$line);
my ($d_num,$d_indic,$d_score,$d_bias,$d_cvalue,$d_ivalue,$d_hmmfrom,$d_hmmto,
$d_hmmbra,$d_alifrom,$d_alito,$d_alibra,$d_envfrom,$d_envto,$d_envbra,$d_acc) = @info;
my $HMMAli = new PirObject::HMMAli();
$HMMAli->set_id($d_num);
$HMMAli->set_score($d_score);
$HMMAli->set_bias($d_bias);
$HMMAli->set_Cvalue($d_cvalue);
$HMMAli->set_Ivalue($d_ivalue);
$HMMAli->set_hmmFrom($d_hmmfrom);
$HMMAli->set_hmmTo($d_hmmto);
$HMMAli->set_hmmBracket($d_hmmbra);
$HMMAli->set_aliFrom($d_alifrom);
$HMMAli->set_aliTo($d_alito);
$HMMAli->set_aliBracket($d_alibra);
$HMMAli->set_envFrom($d_envfrom);
$HMMAli->set_envTo($d_envto);
$HMMAli->set_envBracket($d_envbra);
$HMMAli->set_acc($d_acc);
$alignments->{$d_num} = $HMMAli;
}
elsif ($line =~ m/^\s+==\s+domain\s+(\d+)/) {
$num_dom = $1;
}
else {
$line =~ s/\n$//;
my $HMMAli = $alignments->{$num_dom};
my $ali = $HMMAli->get_ali() || [];
$line =~ s/^\s+//;
push(@$ali,$line);
$HMMAli->set_ali($ali);
}
}
return $all_alignments;
}
sub AddAliToResume {
my ($all_alignments,$Resumes) = @_;
print "Warning: Number of resume != Number of alignments\n" if (scalar(@$Resumes)) != scalar (keys %$all_alignments);
foreach my $Resume (@$Resumes) {
my $SeqIdAndDesc = $Resume->get_SeqIdAndDesc();
my $ali = $all_alignments->{$SeqIdAndDesc};
$Resume->set_alignments($ali);
}
}