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, "2040 days ago
Perl script to split fasta sequence and create 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 $fh, "1969 days ago
1723 days ago
Perl script to run in parellel !
...Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref) = parse_genome...set}{name}, $genome{$chr_set}{nuc_seq}); } }...nstance { my ($chr_set, $chr_seq) = @_; print "starting X...fo->length; my $GCcount = $sequence =~ tr/GC|gc//; my...1684 days ago
1555 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa993 days ago
Bash script to simulate a genome !
...0 conda activate bcftools1.10.2 # Use Seqtk to convert soft-masked base...o compress with bgzip # https://github.com/lh3/seqtk /genetics/elbers/bin/seqtk..._upper.diploid.fasta.gz|\ /genetics/elbers/bin/seqtk/seqtk seq -L0|paste - - |gr...915 days ago
Perl script to find inverted repeats !
...strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::Repe...= "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO-...ome_file, -format => "fasta"); my $seqobj = $seqio->next_seq(); my...ss eq "Inverted") { my $rm_seq = substr($seq, $rm_start-1, $...422 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data415 days ago
Perl script for chi-squared test !
...####################################### # Read sequence file 1 ################...ta = new FAlite(\*FILE); # loop through each sequence in file 1 while(my $ent...while(my $entry = $fasta->nextEntry) { my $seq = uc($entry->seq); # to cou...409 days ago