Results for "TF"
Bio-Scripts
...myDir or full path) $outputDir = "OutDir"; # Path to pattern file $patFile = "/home/anjana/patterns/p...le ends in .fa { print "Processing $seqFile\n"; $outFile = $seqFile; # Crea...2910 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...query => undef, outputFile => undef, database...'o|output_file=s' => \$param{outputFile}, 'd|database=s' =...) ) or !( defined( $param{outputFile} ) ) or !( defined( $...= $count; } open( my $OUTFILE, ">" . $param{outputFile}...2910 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; my $size = 21; my $co...2909 days ago
Blast result parser with Perl and Bioperl
...\n", if (@ARGV != 3); my ($infile,$numHits,$outfile) = @ARGV; print "Parsing...t => 'blast', -file => $infile); open (OUT,">$outfile") or die "Cannot open $out...# get the similarity value printf OUT "%.1f" , ($hsp->frac_cons...2908 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2908 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needlema...2899 days ago
- ...r of sequences >= than the N50 in length: ### my $count = 0; foreach my $v (@sorted) { if($v >= $N50) { $count++; } } printf("N50: $N50 Count >= N50: $cou...
2698 days ago
- ...sub main() { #Define the arguments my ($seqfile, $second, $outfile, $dotfile, $word, $step, $pixels, $t...$xd, $yd, $key, $value); my %TEMPFILE = (); dbmopen(%TEMPFILE, "$dotfile", 0666) || die "Can't open...
2687 days ago
- #!/usr/bin/perl use strict;use warnings; my $i;my $j;my $a; open (FH1,'
2687 days ago
BASH script for SelfBLAST a genome
....sh all #Common settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES THREAD=20 SEQ=""...ry $SEQ -db $MYDB -evalue 1e-5 -num_threads $THREAD -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qen...2646 days ago
