Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database
I am using Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database with following code.Result is printing in command shell but I want result to be write in a file. Please help me to solve this problem.
I want all the results in a text file.
use Bio::Phenotype::OMIM::OMIMparser;
# The OMIM database is available as textfile at:
# ftp://ncbi.nlm.nih.gov/repository/OMIM/omim.txt.Z
# The genemap is available as textfile at:
# ftp://ncbi.nlm.nih.gov/repository/OMIM/genemap
$omim_parser = Bio::Phenotype::OMIM::OMIMparser->new( -genemap => "/path/to/genemap",
-omimtext => "/path/to/omim.txt" );
while ( my $omim_entry = $omim_parser->next_phenotype() ) {
# This prints everything.
print( $omim_entry->to_string() );
print "\n\n";
# This gets individual data (some of them object-arrays)
# (and illustrates the relevant methods of OMIMentry).
my $numb = $omim_entry->MIM_number(); # *FIELD* NO
my $title = $omim_entry->title(); # *FIELD* TI - first line
my $alt = $omim_entry->alternative_titles_and_symbols(); # *FIELD* TI - additional lines
my $mtt = $omim_entry->more_than_two_genes(); # "#" before title
my $sep = $omim_entry->is_separate(); # "*" before title
my $desc = $omim_entry->description(); # *FIELD* TX
my $mm = $omim_entry->mapping_method(); # from genemap
my $gs = $omim_entry->gene_status(); # from genemap
my $cr = $omim_entry->created(); # *FIELD* CD
my $cont = $omim_entry->contributors(); # *FIELD* CN
my $ed = $omim_entry->edited(); # *FIELD* ED
my $sa = $omim_entry->additional_references(); # *FIELD* SA
my $cs = $omim_entry->clinical_symptoms_raw(); # *FIELD* CS
my $comm = $omim_entry->comment(); # from genemap
my $mini_mim = $omim_entry->miniMIM(); # *FIELD* MN
# A Bio::Phenotype::OMIM::MiniMIMentry object.
# class Bio::Phenotype::OMIM::MiniMIMentry
# provides the following:
# - description()
# - created()
# - contributors()
# - edited()
#
# Prints the contents of the MINI MIM entry (most OMIM entries do
# not have MINI MIM entries, though).
print $mini_mim->description()."\n";
print $mini_mim->created()."\n";
print $mini_mim->contributors()."\n";
print $mini_mim->edited()."\n";
my @corrs = $omim_entry->each_Correlate(); # from genemap
# Array of Bio::Phenotype::Correlate objects.
# class Bio::Phenotype::Correlate
# provides the following:
# - name()
# - description() (not used)
# - species() (always mouse)
# - type() ("OMIM mouse correlate")
# - comment()
my @refs = $omim_entry->each_Reference(); # *FIELD* RF
# Array of Bio::Annotation::Reference objects.
my @avs = $omim_entry->each_AllelicVariant(); # *FIELD* AV
# Array of Bio::Phenotype::OMIM::OMIMentryAllelicVariant objects.
# class Bio::Phenotype::OMIM::OMIMentryAllelicVariant
# provides the following:
# - number (e.g ".0001" )
# - title (e.g "ALCOHOL INTOLERANCE" )
# - symbol (e.g "ALDH2*2" )
# - description (e.g "The ALDH2*2-encoded protein has a change ..." )
# - aa_ori (used if information in the form "LYS123ARG" is found)
# - aa_mut (used if information in the form "LYS123ARG" is found)
# - position (used if information in the form "LYS123ARG" is found)
# - additional_mutations (used for e.g. "1-BP DEL, 911T")
my @cps = $omim_entry->each_CytoPosition(); # from genemap
# Array of Bio::Map::CytoPosition objects.
my @gss = $omim_entry->each_gene_symbol(); # from genemap
# Array of strings.
# do something ...
}
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1 answer
Generally speaking, if you want to print to a file, you need to either state that in the command line when running the script using >file.txt or you need to use a file handler in your script.
Considering the second option, what you are looking for is the open command.
use strict;
# Your script here until your first print statement
my $textfile = "/path/to/file.txt";
open ($fh, ">", $textfile) or die "Cannot open $textfile\n";
print $fh "This is the text you want to add to your file\n";
close ($fh);
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