Check if your coputer ready to use BioPerl
#!/usr/bin/perl use strict; use warnings; #bioperl example code use strict; use warnings; #make the bioperl module (class) accessible to your program use Bio::Seq; print"ok - ready to use Bio::Seq";2909 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...ter\n". "Print out the name of sequences with characters other t..."If multiple files are given, sequences in all files are marged..._h)); my $format = "fasta"; my @seqArr = (); @ARGV = ('-') unl...if (defined($opt_m)) { my $seqOut = Bio::SeqIO->new(-fs => \...2906 days ago
2902 days ago
Count GC Content in nucleotide sequence with Perl
..."ID\t% GCContent\tTotal Count\tG Count\tC Count\tA Count\tT Count\n"; $seq = ""; while () { chomp; if (/^>/) { #finish up previous line. if (length($seq) > 0) { &process_it;...2897 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extractSeqbyID.pl LIST FASTA OU...2867 days ago
Extract a range from genome file with perl.
...n/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0];...V[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file => ">$in_file.o...2619 days ago
Perl script to insert sequence in contig !!
# sub signature: #insertSEQintoCONTIGatLOC( SEQ , CONTIG , LOC ) ; sub insertSEQintoCONTIGatLOC{ my ( $SEQ , $CONTIG , $LOC ) = @_; substr( $CONTIG , $LOC , -length($CONTIG) ) = $SEQ ; return $CONTIG; } $s...2700 days ago
2696 days ago
2685 days ago
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq =...-file => ">$file.uniq", -format => "fasta"); while(my $seqs = $seqio->next_seq) { my...2682 days ago