One header for multiple results

lairel has asked for the wisdom of the Perl Monks concerning the following question:

I have the majority of my code running properly, but I am getting repeats of the header for each corresponding output instead of one iteration of the header for all corresponding output. I don't think I am explaining that well, so I have included my current output with the desired output. My code

#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;

unless (open (INFILE, "<", "/scratch/SampleDataFiles/test.fasta")){
        die "Unable to open file", $!;
}

local $/ = ">";
#find and print desired sequence

while (<INFILE>) {

        chomp; #always chomp

                if ( $_ =~ /^(.*?)$(.*)$/ms ) { #match first line as h
+eader

                        my $header = $1; #assign the parts of the matc
+h

                                my $seq = $2;

                        $seq =~ s/\n//g; #get rid of whitespace


                                while($seq =~ /([VILMFWCA]{8,})/g){ #s
+earch for desired sequence

                                        my $location = pos($seq); #fin
+d location

                                                my $length = length($1
+); #determine length

                                                print "Hydrophobic str
+etch found in: ", $header, "\n"; #printing outputs for results

                                                print $1, "\n";
                                        print "The match was at positi
+on: ", $location - $length + 1, "\n\n";

                                }



                }
}
close INFILE;
[download]

The output is supposed to look like this:

Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;

 

AVVAAVMW

The match was at position: 325

 

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 | Name=DISP2; Synonyms=DISPB, KIAA1742;

 

VAVLMLCLAVIFLC

The match was at position: 170

 

LLALVAIFF

The match was at position: 493

 

IWICWFAALAA

The match was at position: 705

 

LALALAFA

The match was at position: 970
[download]

but my current output is like this:

Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 365 |    Name=HLA-A; Synonyms=HLAA;

AVVAAVMW

The match was at position: 325

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

VAVLMLCLAVIFLC

The match was at position: 170

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

LLALVAIFF

The match was at position: 493

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

IWICWFAALAA

The match was at position: 705

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

LALALAFA

The match was at position: 970
[download]

I'm so close

Comment on One header for multiple results Select or Download Code

Replies are listed 'Best First'.
Re: One header for multiple results by AppleFritter (Vicar) on Oct 21, 2015 at 14:51 UTC
Well, you ARE outputting the "Hydrophobic stretch found" line each time there is a match: `while($seq =~ /([VILMFWCA]{8,})/g){ #search for desired sequence my $location = pos($seq); #find location my $length = length($1); #determine length print "Hydrophobic stretch found in: ", $header, "\n"; #printing o +utputs for results print $1, "\n"; print "The match was at position: ", $location - $length + 1, "\n\ +n"; }` [download] If you only want to print it once, the easiest way is to introduce a flag indicating whether it's already been output. Declare a new variable in front of your while loop there, and then check and set it inside the loop body: `my $header_printed = 0; # header for this thingamabob was not yet prin +ted while($seq =~ /([VILMFWCA]{8,})/g){ #search for desired sequence my $location = pos($seq); #find location my $length = length($1); #determine length unless($header_printed) { print "Hydrophobic stretch found in: ", $header, "\n"; #printi +ng outputs for results $header_printed = 1; } print $1, "\n"; print "The match was at position: ", $location - $length + 1, "\n\ +n"; }` [download] Obviously this could be written more concisely, but this way it's clear what's going on. Does this help you?	[reply] [d/l] [select]
Re^2: One header for multiple results by lairel (Novice) on Oct 21, 2015 at 15:09 UTC
Thank you! It did exactly what I wanted.	[reply]
Re: One header for multiple results by AnomalousMonk (Archbishop) on Oct 21, 2015 at 15:00 UTC
This thread seems to be a continuation of Where am I going wrong?. lairel: It would have been nice if you had yourself included a link to the previous thread. Please see What shortcuts can I use for linking to other information?. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l]
Re: One header for multiple results by Laurent_R (Canon) on Oct 21, 2015 at 14:40 UTC
It would be much easier to answer if you provided a sample of your input data, as it would help finding out where your code is wrong. Without that, we can only make wild guesses or shots in the dark. I would also suggest that you use indentation consistently, it would probably help yourself finding out what you're doing wrong.	[reply]
Re: One header for multiple results by GotToBTru (Prior) on Oct 21, 2015 at 14:58 UTC
You have the line that prints the header in your inner while loop. Of course you get it with every sequence. Move that statement to before your loop, and you will see it only once. Dum Spiro Spero	[reply]
Re^2: One header for multiple results by lairel (Novice) on Oct 21, 2015 at 15:08 UTC
I had tried that, but then it would bunch the headers before the results. I appreciate the suggestion!	[reply]
Re^3: One header for multiple results by GotToBTru (Prior) on Oct 21, 2015 at 15:11 UTC
Not if you did what I suggested ... but I see in the end you have an answer. Dum Spiro Spero	[reply]