Results for "header"
Bio-Scripts
Blast result parser with Perl and Bioperl
....."; my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile); open (OUT,">$outfile") or die "Cannot open $outfile: $!"; # print the header info for tab-deliminated colu...2908 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2908 days ago
- P
2865 days ago
- #!/usr/bin/perl #use strict; #use warnings; #Author: Santhilal Subhash #Contact: santhilal.subhash@gu.se #RPKM for RNAseq V1.3 #USAGE for sample input provided: p...
2865 days ago
Extracting FASTA sequences based on position with perl script !!
...$/ = '>'; while () { chomp; next unless /(.+)/; my ($header) = "$/$1_$start-$end\n"; my $seq = ${^POSTMATCH}; $seq =~ s/\s//g; print $header; print +( substr $seq, $...2615 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2610 days ago
Extract fasta sequence from a multifasta file with coordinates
...0 => 4_100_000); my $revseq = $db->seq('CHROMOSOME_I', 4_100_000 => 4_000_000); my $length = $db->length('CHROMOSOME_I'); my $header = $db->header('CHROMOSOME_I'); my $alpha...2525 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print...2524 days ago
Extract fasta sequence from a multifasta file with fasta header Ids
#!/usr/bin/perl use strict; use warnings; #Usage: perl my $list = shift @ARGV; my $fasta = shift @ARGV; my $out = shift @ARGV; my %select; open LIST,...2511 days ago
- #!usr/bin/perl use strict; use warnings; my %id2seq = (); my $id = 0; open F,"$ARGV[0]",or die $!; while(){ chomp; if(...
2506 days ago
