In article <36663A9C.29A06C4D at mailer.uni-marburg.de> Andreas Doll <doll at mailer.uni-marburg.de> writes:
>How can I import sequences in FASTA format into the staden package.
>Is there a possibility to covert it into a SCF file?
We cannot directly load FASTA files (although it would appear to be a most
obvious thing to add!). We can load plain text files though, with no
header at all. So just strip off the ">id" bit from the fasta file.
If you have one single fasta file with lots of entries, then try using
the fasta2exp script, held in $STADENROOT/src/scripts. If you don't
have a copy of it, here it is.
James
#!/usr/bin/nawk -f
BEGIN {
file="";
}
/^;/ {
next;
}
/^>/ {
gsub(">", "");
if (file != "") {
print "//" >> file;
close(file);
}
file=$1".exp";
print "ID "$1 > file;
print "SQ" >> file;
print "Creating", $1;
next;
}
{
print " "$0 >> file;
}
END {
print "//" >> file;
close(file);
}
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/
