Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAA...2844 days ago
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CONTIG , $LOC , -le...2701 days ago
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2685 days ago
Perl script to insert the DNA string in genome
...) my $out = $ARGV[1]; # output fasta file my $chr="test"; #insertion chromosome my $pos=10; # position of the insertion my $seqI = "AAAA"; #sequence of the insertion my $seq_i...2651 days ago
BASH script for SelfBLAST a genome
...-out $MYDB fi if [ $1 = "extract" ] then echo "Extracting the sequence $2 for you from $FASTAFILE --...$2.fa SEQ=$2.fa elif [ $1 = "all" ] then echo "You want entire sequence to blast" SEQ=$FASTAFILE...2644 days ago
Extract fasta sequence from a multifasta file with coordinates
...mary_ids; foreach my $id (@ids) { my $sequence = $db->seq($id, $querySizeST => $querySizeED); if (!defined( $sequence )) { die "Sequen...b->alphabet('CHROMOSOME_I'); # Access to sequence objects. See Bio::PrimarySeqI...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,...2510 days ago
Compress and decompress the sequence with perl
use strict; use warnings; my @char; while () { @char = split //; } comp(\@char); #--------------------- my $com= "r0a3m4a4j0"; my @com = split //, $com; dcomp (\@com); #dcomp sub here sub dcomp { my ($com_ref)=@_; my @com=@$com_ref; my $car; for (my $aa=0; $aa2507 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2460 days ago