Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2243 days ago
Perl script to read multi fasta sequence one by one
...ile $!"; print OUT "$key\n$fastaSeq{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multipl...2225 days ago
Biological Sequence handling with Perl !
...return $s; } sub longest_orf { my $self = shift; my ($max,$pos,$frame); foreach (-3..-1...1) > length($max)) { $max = $1; $frame = $_; $pos = pos($translation) - length(...2185 days ago
Perl script to find coding regions in DNA sequences
...the hash table $pcodons{$codon}=$freq; } close(PROPCODONS); ############...use a var to save the whole sequence inside close(SEQUENCE); # concat every...e obtained with the two sequences: high values (positive) for coding protein sequ...2159 days ago
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Perl script to count number of Ns in a multifasta file !
...f(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n"; } } close(I); __END__ Note: Conv...2148 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2148 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...r}{seq}\n>@$SeqIds[$cnt]\n$refSeq->{@$SeqIds[$cnt]}{seq}\n"; close $ofh or die "Could not close file '$tmpFile' $!"; $cnt...{$seqid}{nonatgc} += ($line =~ tr/N/N/); } } close $fh; return \%sequences...2144 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2144 days ago