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, "2136 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 here...2132 days ago
Perl script to convert GFF 2 FASTA !
...fasta" ); ###### Output type description ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cdna - transcribed sequence (devoid of introns, but conta...2131 days ago
2118 days ago
2115 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1;...2088 days ago
2067 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift...2058 days ago
Perl script to break the contigs by 'N'
...AFF,">$ARGV[0].parts.scaff"); while ( my $seqobj = $fasta->next_seq() ) { #gets contig id my $contig = $seqobj->display_id(); #gets contig sequence my $seq = $seqobj->seq; m...2055 days ago
Perl script to split fasta sequence / overlaps
#!/usr/bin/perl use strict; use warnings; my $len = 5000; my $over = 200; my $seq_id=$ARGV[0]; my $seqFile = $ARGV[1]; my $seq; open(my $fh, "2035 days ago