Lecture 16

ftp http://www.bx.psu.edu/~anton/share/bmmb598f/lecture15.tar.gz
gunzip -c lecture15.tar.gz | tar xvf -

Program for creating DNA files:

#! /usr/bin/perl -w

$i = 0;

while (<STDIN>) {
    chop;
    @tmp = split /\t/, $_;
    open (OUT, ">dna.$i.faa") or die "Cannot create file.$i.fna:$!\n";
    print OUT ">$tmp[0]\n";
    print OUT "$tmp[4]\n";
    print OUT ">$tmp[1]\n";
    print OUT "$tmp[5]\n";
    close OUT;
    ++$i;
}

Run this command:

cat h_w_ProtCDS.txt | perl createClustalFilews.pl

Run this command:

ls -1 dna.* > files.dna ; ls -1 prot*.pir > files.prot ; paste -d " " files.prot files.dna | sed s/^/cat\ / | sed s/$/\ \|\ perl\ Fasta2Tab\.pl\ \>\ / > ttt ; paste -d " " ttt files.dna | sed s/$/\.conc/ > concatenate
chmod 755 concatenate

HYPHY