2707 days ago
2696 days ago
Perl script to remove the duplicate sequences from multifasta file
..."myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->new(-file => ">$file.uniq", -format => "fasta"); while(my $seqs = $seqio...2692 days ago
Perl script to insert the DNA string in genome
...io::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fasta file my $chr="test"; #inse...e insertion my $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file); my $seq_ou...2661 days ago
Calculate ATGC percentage in parallel with perl
...el::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fasta"); while(my$seqobj = $seqio-...2658 days ago
BASH script for SelfBLAST a genome
...ast.sh extract #USAGE: ./selfBlast.sh all #Common settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES T...eating creating blastDB named $MYDB for you"; makeblastdb -in $FASTAFILE -parse_seqids -dbtype nuc...2654 days ago
Calculate some statistics for a DNA alignment with Perl
...rint $jcmatrix->print_matrix; ## and for measurements of synonymous /nonsynonymous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta',...2652 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 () {...2624 days ago
Palindrome Simulation commands !
...mands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101.fasta id=97 3316 mutate.sh in=mu...55_template_pass_FAH31515.faa mutant3CH101.fasta mutant15CH101.fasta mutant153...tk seq -a interleavedPE.fq > interleavedPE.fasta 3323 ~/Tools/BWISE/Bwise.p...1738 days ago
Extract fasta sequence from a multifasta file with coordinates
...!/usr/bin/perl use Bio::DB::Fasta; #USAGE perl extractFASTAwithSIZE.pl finalSample_filter...d.fa 0 1000 > aaaaaa.fa my $fastaFile = shift; my $querySizeST...} __END__ use Bio::DB::Fasta; # Create database from...le access my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/...2535 days ago