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On Feb 11, 2004, at 10:34 AM, Michael S. Robeson II wrote:
Hey, thanks again for the perl code.
You're welcome, but let's keep our discussion on the mailing list so we
can all help and learn.
However, I forgot to take into account that the original input
On Feb 5, R. Joseph Newton said:
>my $sequence_length = 20;
>my $line = ;
>chomp $line;
>while ($line) {
> my $sequence_tag = trim_line($line);
> $line = ;
> chomp $line;
> my @nucleotides = split //, $line;
> push @nucleotides, '_' for (1..($sequence_length - @nucleotides));
I'd be in
"Michael S. Robeson II" wrote:
> Hi I am all still to new to PERL and I am having trouble playing with
> formatting my data into a new format. So here is my problem:
>
> I have data (DNA sequence) in a file that looks like this:
>
>
> # Infile
>
> >bob
> AGTGATGCCGACG
> >fred
> ACGCATA
On Feb 4, Michael S. Robeson II said:
> >bob
>AGTGATGCCGACG
> >fred
>ACGCATATCGCAT
> >jon
>CAGTACGATTTATC
>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
>
>
>The "R 1" is sta
On Feb 4, 2004, at 11:35 AM, Michael S. Robeson II wrote:
Hi I am all still to new to PERL and I am having trouble playing with
formatting my data into a new format. So here is my problem:
I have data (DNA sequence) in a file that looks like this:
# Infile
>bob
AGTGATGCCGACG
>fred
ACG
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 -
Michael S. Robeson II wrote:
>
> Hi I am all still to new to PERL and I am having trouble playing with
> formatting my data into a new format. So here is my problem:
>
> I have data (DNA sequence) in a file that looks like this:
[snip]
Please don't talk about interesting stuff like DNA sequences o
