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parse_hmmsearch - parse single/multiple HMMSEARCH results file(s) with
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different output options
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parse_hmmsearch [--po] [--ps] -s hmmsearch_file
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parse_hmmsearch [--po] [--ps] -m index_file
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=head2 Mandatory Options:
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-s HMMSEARCH file to parse.
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-m INDEX file that contains a list of HMMSEARCH files for multiple
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=head2 Special Options:
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--po Print only the hits that have positive scores.
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--ps Print the total of positive scores found.
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--help Show this documentation.
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to the
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Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via the
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https://redmine.open-bio.org/projects/bioperl/
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Mauricio Herrera Cuadra <mauricio at open-bio.org>
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# Modules, pragmas and variables to use
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use vars qw($opt_s $opt_m $opt_po $opt_ps $opt_help);
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# Gets options from the command line
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GetOptions qw(-s:s -m:s --po --ps --help);
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# Print documentation if help switch was given
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exec('perldoc', $0) and exit() if $opt_help;
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# If no mandatory options are given prints an error and exits
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if (!$opt_s && !$opt_m) {
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print "ERROR: No HMMSEARCH or INDEX file has been specified.\n Use
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'--help' switch for documentation.\n" and exit();
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} elsif ($opt_s && $opt_m) {
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print "ERROR: You must select only one option (-s or -m) for input.\n
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Use '--help' switch for documentation.\n" and exit();
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# Initializes a counter for the domain positive scores if the option
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my $pos_scores = 0 if $opt_ps;
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# If single file mode was selected
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parse_hmmsearch($opt_s);
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# Prints the total domain positive scores if the option was given
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print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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print "Total domain positive scores: $pos_scores\n";
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# If multiple files mode was selected
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# Opens the INDEX file sent as input
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open(FH, "<", $opt_m) or die("Unable to open INDEX file: $opt_m ($!)");
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# Cycle that extracts one line for every loop until finding the
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while (my $line = <FH>) {
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# Deletes the new line characters from the line
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# Parses the result file in turn
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parse_hmmsearch($line);
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print "= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
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# Prints the total domain positive scores if the option was given
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print "Total domain positive scores: $pos_scores\n" if $opt_ps;
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# Subroutine that parses a HMMSEARCH results file
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sub parse_hmmsearch {
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# Gets the parameters sent to the function
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# Creates a new Bio::SearchIO object
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my $in = new Bio::SearchIO(
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# Loops through the results file
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while (my $result = $in->next_result()) {
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# Prints program name and version (these are values from
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# Bio::Search::Result::GenericResult methods)
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print $result->algorithm(), " ", $result->algorithm_version(), "\n";
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print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# Prints HMM file and sequence database (these are values from
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# Bio::Search::Result::HMMERResult methods)
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print "HMM file:\t\t\t", $result->hmm_name(), "\n";
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print "Sequence database:\t\t", $result->sequence_file(), "\n";
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print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# Prints some values from Bio::Search::Result::GenericResult
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print "Query HMM:\t\t\t", $result->query_name(), "\n";
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print "Accession:\t\t\t", $result->query_accession(), "\n";
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print "Description:\t\t\t", $result->query_description(), "\n";
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print "Total hits:\t\t\t", $result->num_hits(), "\n";
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# Loops through the sequence in turn
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while (my $hit = $result->next_hit()) {
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# If only positive scores option was given and the score
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# in turn is greater than zero
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printHits($hit) if ($hit->score() >= 0);
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# Prints all hits otherwise
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# Subroutine that prints the values from a Bio::Search::Hit::HitI
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# Gets the parameters sent to the function
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# Prints some values from Bio::Search::Hit::HitI methods
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print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n";
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print "Hit ", $hit->rank(), "\n";
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print "Sequence:\t\t\t", $hit->name(), "\n";
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print "Description:\t\t\t", $hit->description(), "\n";
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print "Score:\t\t\t\t", $hit->score(), "\n";
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print "E-value:\t\t\t", $hit->significance(), "\n";
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print "Number of domains:\t\t", $hit->num_hsps(), "\n";
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# Loops through the domain in turn
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while (my $hsp = $hit->next_hsp()) {
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# Prints some values from Bio::Search::HSP::HSPI methods
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print " - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n";
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print " Domain:\t\t\t", $hsp->rank(), " of ", $hit->num_hsps(), "\n";
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print " seq-f:\t\t\t", $hsp->start('hit'), "\n";
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print " seq-t:\t\t\t", $hsp->end('hit'), "\n";
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print " hmm-f:\t\t\t", $hsp->start(), "\n";
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print " hmm-t:\t\t\t", $hsp->end(), "\n";
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print " score:\t\t\t", $hsp->score(), "\n";
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$pos_scores++ if ($hsp->score() >= 0) && $opt_ps;
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print " E-value:\t\t\t", $hsp->evalue(), "\n";
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my $hmm_string = $hsp->query_string();
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$hmm_string =~ s/<-\*$//;
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print " hmm string:\t\t\t", $hmm_string, "\n";
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print " homology string:\t\t", $hsp->homology_string(), "\n";
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print " hit string:\t\t\t", $hsp->hit_string(), "\n";
added
removed
scripts/searchio/parse_hmmsearch.PLS
