[Omaha.pm] Could you take a look

[kiran bina]

I don't know if i did not formulate the problem right. This is what I
wanted.
The GI- number in File2 is a smaller subset of possible GI-in File 1 (This
has the matching GI plus the sequence I am interested in).
(Or. I want to pull all the sequences from file-1 using the GI listed in
File 2)
kiran

On 1/19/07, Jay Hannah <jay at jays.net> wrote:
>
> On Jan 19, 2007, at 7:18 AM, kiran bina wrote:
> > Could you please take a look at this.
> > <test.zip>
>
> Hi again Kiran.  :)
>
>
> Your code (as viewed in the debugger):
>
>
>    DB<6> l 9-15
> 9:      while (my $line=<IN1>)
> 10      {
> 11:         if ($line=~ m/\>\s+/)
> 12          {
> 13:             $line=~ m/^(\S+)\>\s(\S+)$/;
> 14==>           my $read = $1;
> 15:             my $value= $2;
>
>
> Your first problem is that $line has carriage returns and/or newlines
> at the end, so your regex demand that the line end with \S+ fails.
>
> I'll step past the regex and show you the newlines:
>
>
>                                                   main::(test.pl:
> 13):             $line=~ m/^(\S+)\>\s(\S+)$/;
>
> DB<1> n
> main::(test.pl:14):             my $read = $1;
>
>
>
>
>
>       DB<3> p "[$line]"
> [a> APPLE
> ]
>
>
> Now normally you could just 'chomp $line;', but that didn't work for
> me on your data. Perhaps because my Mac defines newlines differently
> than wherever you made your file? Even after I added chomp it still
> wasn't working, so I x'd it in the debugger to see why not:
>
>
>    DB<3> x $line
> 0  "a> APPLE\cM"
>
>
> Bummer. I believe "\r\n" (carriage return, linefeed) is interpreted
> as Control-M, So I added a regex to remove all carriage returns and
> linefeeds
>
>
>      $line =~ s/[\r\n]//g;
>
>
> (chomp might work fine for you.)
>
> The next annoyance was all these warnings:
>
>
> Use of uninitialized value in string eq at test.pl line 43, <IN1>
> line 5.
>
>
> Which you can avoid by NOT running look_up_order() if there is no
> $value. I don't know if that's what you wanted to do or not, but you
> can do that with this line
>
>
>          next unless ($value);  #  No value in file...
>
>
> So your code now reads like this:
>
>
> while (my $line=<IN1>)
> {
>      $line =~ s/[\r\n]//g;
>      if ($line=~ m/\>\s+/)
>      {
>          $line=~ m/^(\S+)\>\s(\S+)$/;
>          my $read = $1;
>          my $value= $2;
>          next unless ($value);  #  No value in file...
>
>
> which seems to work?
>
>
> $ perl test.pl
> a
> APPLE
> b
> BOY
> d
> DOG
>
>
> ?
>
> Lower, your look_up_order() doesn't seem to do anything at all. Were
> you wanting it to pull values out of File2 if File1 didn't have a
> $value or something?
>
> HTH,
>
> j
>
>
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-- 
Dhundy R. Bastola
Assistant Professor
Department of Pediatrics
University of Nebraska Medical Center
Omaha NE 68198
Always reply to: dbastola at unmc.edu
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