Perl script to count number of Ns in a multifasta file !
...,"\t",$n/($l-$n),"\n"; } } close(I); __END__ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl cou...2186 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2186 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2182 days ago
Perl script to convert GFF 2 FASTA !
...>new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outfile_upstream3000 = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ######...2181 days ago
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Installing Porechop on Ubuntu !
...esolving deltas: 100% (869/869), done. Checking connectivity... done. ➜ Tools git:(master) ✗ cd Porechop ➜ Porechop git:(master) python3 setup.py install running install...2148 days ago
2141 days ago
Install Python locally on shared Linux server !
...n command, it will use the default python of #the system. We are going to update the environment variables...ofile #You might need to logout and login again for the environment to update properly. At this point,...2140 days ago