Perl script to insert the DNA string in genome
...:SeqIO->new( -format => 'fasta',-file => $file); my $seq_out = Bio::SeqIO->new( -format => 'fasta',-file => ">".$out); while( my $seq = $seq_in->next_seq() ) { if($seq->...2674 days ago
Calculate ATGC percentage in parallel with perl
...format => "fasta"); while(my$seqobj = $seqio->next_seq) { my $id = $seqob...value $sequences{$id} = $seq; } my $max_procs = 5; my @names = key...hen a child finishes up so we can # get it's exit code $pm->run_on_finish...2671 days ago
BASH script for SelfBLAST a genome
...bin/bash #self BLAST a genome -- Expecting you have blast and sam...dra Narayan #USAGE: ./selfBlast.sh extract #USAGE: ./selfBlast.sh...base for MergedContigs.fasta genome exists" else echo "Thanks fo...e nucl -out $MYDB fi if [ $1 = "extract" ] then echo "Extrac...2667 days ago
Extract a range from genome file with perl.
...ew ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file => ">$in_file.out", -format => 'fasta'); while (my $seq = $in->next_seq() ) { $seq->displ...2642 days ago
Calculate some statistics for a DNA alignment with Perl
...ta/insulin.water'); my $aln = $alignin->next_aln; my $jcmatrix = $stats->distance(-align =>..._gojobori_test.aln'); my $alnobj = $in->next_aln; my ($seq1id,$seq2id)...; for (sort keys %$an ){ next if /Seq/; printf(...2664 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end...pop; my $start = pop; local $/ = '>'; while () { chomp; next unless /(.+)/; my ($hea...2636 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2632 days ago
Extract ids from file with perl
#!/usr/bin/perl use strict; use warnings; my $fh=read_fh("fin.txt"); my %idHash; my $lastKey; whi...cutiry -- might does not finish all steps delete $hash{$allIds[-1]}; next if exists $hash{$look_for};...2623 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/pic...1352 days ago
Extract fasta sequence from a multifasta file with coordinates
#!/usr/bin/perl use Bio::DB::Fasta; #USAGE perl extractFASTAwithSIZE.pl finalSample_filtered.fa 0...my $stream = $db->get_PrimarySeq_stream; while (my $seq = $stream->next_seq) { # Bio::PrimarySe...2547 days ago