Finding Kmers from fasta sequence file
Save it in sample.fa >test TAATGCCATGGGATGTT jellyfish count -m 3 -s 100000 sample.fa -o sample.jf jellyfish dump -c sample.jf It return TGT 1 GAT 1 GGG 1 GGA 1 CAT 1 TGC 1 TAA 1 GCC 1 CCA 1 GTT 1 TGG 1 ATG 3 AAT 12033 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, "2033 days ago
Split the multifasta in separate files !
cat Avaga_allPalindrome.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'2018 days ago
Backward Elimination with Python
#Backward Elimination with p-values only: import statsmodel...regressor_OLS = sm.OLS(y, x).fit() maxVar = max(regre...X_opt, SL) #Backward Elimination with p-values and Adjusted R Squa...regressor_OLS = sm.OLS(y, x).fit() maxVar = max(regre...2016 days ago
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my ( $word) = m/(\...1961 days ago
1861 days ago
Resume the MIRA assembler run !
...assembly -h / --help Print short help and exit -v / --version Print version and exit...1795 days ago
1786 days ago
1786 days ago
Perl script to run in parellel !
...uc_seq}); } } } $pm->finish; } $pm->wait_all_children; sub output_e...{ my ($chr_set, $chr_seq) = @_; print "starting XFOIL instance with parameters $chr_set!\n";...1747 days ago