Results for "my"
Bio-Scripts
Calculate ATGC percentage in parallel with perl
...#usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqIO->new(-fil...ay_id; # there's your key my $seq = $seqobj->seq;...$pm->run_on_finish ( sub { my ($pid, $exit_code, $ident) =...e pool!\n"; sub checkATCG { my $name=shift; my $DNA=$sequen...2706 days ago
BASH script for SelfBLAST a genome
...ommon settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES THREAD=20...ript $USER; Me creating creating blastDB named $MYDB for you"; makeblastdb -i...ting"; blastn -task megablast -query $SEQ -db $MYDB -evalue 1e-5 -num_threads $...2702 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $e...y $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file...2677 days ago
Calculate some statistics for a DNA alignment with Perl
...o::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(...> 't/data/insulin.water'); my $aln = $alignin->next_aln;...onymous substitutions ## my $in = Bio::AlignIO->new(-form...$results->[0]{$_}); } my $results2 = $stats->calc_all_...2699 days ago
- ...in/perl use strict; use warnings; #For normal overlaps my ($lower, $upper) = (40, 100); for my $num (17,42,99,111) {...s #!/usr/bin/perl use strict; use warnings; use 5.010; my ($lower, $upper) = (40, 100);...
2686 days ago
Check overlapping range with Perl
...rl use strict; use warnings; my @ranges = 0; push @ranges, $...] + 1 + int rand 200 for 1..10000; my @tests = map int rand $ranges...ranges, \@tests); sub div { my ($border, $tests) = @_;...} } else { my $pivot = int((@$ranges + 1)/...2677 days ago
Extracting FASTA sequences based on position with perl script !!
...: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'...next unless /(.+)/; my ($header) = "$/$1_$start-$end\n"; my $seq = ${^POSTMATCH}; $s...2672 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; while () { chomp $_; my @cells = split /\t/, $_; $idHash...######### #Open and Read a file sub read_fh { my $filename = shift @_; my...2658 days ago
Extract fasta sequence from a multifasta file with coordinates
...iltered.fa 0 1000 > aaaaaa.fa my $fastaFile = shift; my $querySizeST = shift; my $qu...>get_all_primary_ids; foreach my $id (@ids) { my $sequenc...om a directory of Fasta files my $db = Bio::DB::Fasta->n...bseq(4_000_000 => 4_100_000); my $trunc = $seq->trunc(4_000_...2582 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2575 days ago
