Michael S. Robeson II wrote:
> I have data (DNA sequence) in a file that looks like this:
>
> ####
> # Infile
> ####
> >bob
> AGTGATGCCGACG
> >fred
> ACGCATATCGCAT
> >jon
> CAGTACGATTTATC
>
> and I need it converted to:
>
> ####
> # Outfile
> ####
> R 1 20
>
> A G U G A T G C C G A C G - - - - - - - bob
> A C G C A U A U C G C A U - - - - - - - fred
> C A G U A C G A U U U A U C - - - - - - jon
there are many ways of doing that. here is one:
#!/usr/bin/perl -w
use strict;
#--
#-- discard the first 3 header lines
#--
<DATA> for 1..3;
#--
#-- read each ' >'
#--
$/ = ' >';
while(<DATA>){
next unless(my($n,$s) = /(.+)\n(.+)/);
#--
#-- pad dna sequence to 20 bytes and translate T to U
#-- here, you will prompt the user to enter a number instead
#--
($s .= '-'x(20-length($s))) =~ y/T/U/;
#--
#-- put space after each character
#--
$s =~ s/./$& /g;
print "$s\t$n\n";
}
__DATA__
####
# Infile
####
>bob
AGTGATGCCGACG
>fred
ACGCATATCGCAT
>jon
CAGTACGATTTATC
__END__
prints:
A G U G A U G C C G A C G - - - - - - - bob
A C G C A U A U C G C A U - - - - - - - fred
C A G U A C G A U U U A U C - - - - - - jon
david
--
sub'_{print"@_ ";* \ = * __ ,\ & \}
sub'__{print"@_ ";* \ = * ___ ,\ & \}
sub'___{print"@_ ";* \ = * ____ ,\ & \}
sub'____{print"@_,\n"}&{_+Just}(another)->(Perl)->(Hacker)
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