perl?

[semna]

Hi,
I have a file like this:
ID : 741158
PARENT ID : 9605
RANK : species
GC ID : 1
MGC ID : 2
SCIENTIFIC NAME : Homo sp. Altai
GENBANK COMMON NAME : Denisova hominin
//
ID : 756884
PARENT ID : 9598
RANK : subspecies
GC ID : 1
MGC ID : 2
SCIENTIFIC NAME : Pan troglodytes ellioti
//
I need just ID number if rank :species. so for this example the uotput should be :741158.
my perl script is like this:
#!/usr/bin/perl -w
use strict;
use warnings;


open (FILE, 'm.txt');
while (my $p = <FILE>){
if ($p =~ /^\/\/\n/){
last;
}elsif ($p =~ /GC ID : 1/){
next;
}elsif ($p =~ /MGC ID : 2/){
next;
}elsif ($p =~ /SCIENTIFIC NAME :\D/){
next;
}elsif ($p =~ /\bspecies$/){
print "ID number";?????
}
}

Any sugeestion? Thanks.

[thurisaz]

This should work if the file is formatted exactly as you've shown:

open (FILE, 'm.txt');
while(<FILE>) {
  if ($_ =~ m/^ID :/ ) {
    @id = split(/ : /,$_);
  }
  if ($_ =~ m/\bspecies$/) {
    print $id[1];
  }
}

Note that it's pretty fragile -- it doesn't do any checking and assumes the input is just as you've shown. In particular: (1) Every record must have an ID; (2) the ID must always come before the rank; (3) the ID line must have a space, colon, space and then the ID number; (4) Any line that ends with the word "species" will cause the ID to be printed, so "subspecies" (etc) must always be one word and "species" shouldn't appear as the final word of any other line.

[semna]

Hi thurisaz,
Thanks for your answer. All your assumptions are true but your code is not working.

[thurisaz]

Hi,

Just to be clear: I omitted the initial "#!/usr/bin/perl -w" line. If you want to copy & paste into a file, you will need to include that, like this:

#!/usr/bin/perl -w

open (FILE, 'm.txt');
while(<FILE>) {
  if ($_ =~ m/^ID :/ ) {
    @id = split(/ : /,$_);
  }
  if ($_ =~ m/\bspecies$/) {
    print $id[1];
  }
}

If that code isn't working for you, then please let me know what exactly is going wrong. I just copied & pasted to be sure and it seems to work fine.

[semna]

I just copy your code but the error is :
Use of uninitialized value in print at 110.pl line 13, <FILE> line 3
for that I defined array and variable ID (my) but noting change.
Thanks.

[thurisaz]

An entry at around line 13 in your file (m.txt) is breaking the script; it seems like it's because there is a line that ends in "species" _before_ an ID has been provided. Like I said, it's a fragile script that assumes everything is well-behaved. A few changes will make sure that ID has been assigned before printing and also clears the ID at the end of each record:

#!/usr/bin/perl -w

open (FILE, 'm.txt');
while(<FILE>) {
    if ($_ =~ m/^ID :/ ) {
      @id = split(/ : /,$_);
    }
    if ($_ =~ m/\bspecies$/ && $id[1]) {
      print $id[1];
    }
    if ($_ =~ m?^//$?) {
      $id[1]=0;
    }
}

It sounds like you have something unexpected going on with your input file, though, so I strongly recommend having a good look at it, especially since the script makes so many assumptions.

[semna]

Thanks but it is still not working. Each time I just used exactly that file posted on this page.It is really strange. But anyway thanks so much for your help.

[labunit]

I just copy your code but the error is :
Use of uninitialized value in print at 110.pl line 13, <FILE> line 3
for that I defined array and variable ID (my) but noting change.
Thanks.

Make sure you define your id-array with

my @id;

and not

my $id;

If this is not it, just copy & paste your code here.

[severin]

unix script

ID : 741158
PARENT ID : 9605
RANK : species
GC ID : 1
MGC ID : 2
SCIENTIFIC NAME : Homo sp. Altai
GENBANK COMMON NAME : Denisova hominin
//

At the command prompt you can

more filename.txt | egrep ID | awk '{print :$3}' | more
that will give you your list. of IDs and the colon in front.