Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #...base => undef, returnType => undef, maxRecords =>...m{database}, 'r|return_type=s' => \$param{returnType},...); $param{query} = uri_escape( $param{query} ); _doSearc...tmax = $count; } open( my $OUTFILE, ">" . $param{o...2927 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w ################################...################ #MLP neural network in Perl Original source code by Phil Brierley #Translated into perl - ccolbourn Oct 2004 #####...LR_HO = 0.07; ################ Data dependent settings ######### my $...2927 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Util qw/ shuffle /; my $outputfile = 'randomoutput.txt'; open my $in_fh, '', $outputfile;...2926 days ago
2921 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under G...$in = Bio::SearchIO->new(-format => 'blast', -file => $infile); open (OUT,">$outfile") or die "Cannot open $outfile: $!"; # print th...2926 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fast...th characters other than ATGC-.\n". "If -m is specified, the ambiguous characters are repleced with the\n". "specified character. e.g. -m '?'...2926 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2926 days ago
2926 days ago
Perl to print indivisual nucleotide from a sequence!
#!/usr/bin/perl use strict; use warnings; my $string = "ATGCTTGCGT?AAATG??CT?GCGTA"; my @chars = split("", $string); print "First character: $chars[0]\n";2925 days ago
2920 days ago