CODEWITHSUNDEEP
perltextformatting
B.Hall
B.Hall

Reputation: 25

Removing Spaces in Perl when Printing to a text file

So I have this code in perl that parses an xml and i want the perl file to print out to the text file so that everything is in columns like so:

SpectrumIndex TotalIonCount Duration Spectrum 
Integer Float Float mass,abundance;mass1,abundance1;mass 2,abundance1

Here is the xml code:

<message>
       <cmd id="result_data">
          <result-file-header>
                 <path>String</path>
                 <duration>Float</duration>
                 <spectra-count>Integer</spectra-count>
          </result-file-header>
          <scan-results count="Integer">
                 <scan-result>
                 <spectrum-index>Integer</spectrum-index>
                 <time-stamp>Integer</time-stamp>
                 <tic>Float</tic>
                 <start-mass>Float</start-mass>
                 <stop-mass>Float</stop-mass>
                 <spectrum count="Integer">mass,abundance;mass1,abundance1;
                 mass2,abundance2;mass6,abundance6</spectrum>
                 </scan-result>
                 <scan-result>
                 <spectrum-index>Integer</spectrum-index>
                 <time-stamp>Integer</time-stamp>
                 <tic>Float</tic>
                 <start-mass>Float</start-mass>
                 <stop-mass>Float</stop-mass>
                 <spectrum count="Integer">mass3,abundance3;mass4,abundance4;
                 mass5,abundance5</spectrum>
                 </scan-result>
            </scan-results>
    </cmd>
</message>

However using the following perl code:

#!/usr/bin/perl-w
#example to write to text
my $file = "gapiformat.txt";
unless(open FILE, '>'.$file) {
    die "\nUnable to create $file\n";
}
use strict;
use warnings;
use XML::Simple;
use Data::Dumper;


 my $values= XMLin('samplegapi.xml',ForceArray => ['scan-result','result-file-header']);


my $results = $values->{'cmd'}->{'scan-results'}->{'scan-result'};
my $results1= $values->{'cmd'}->{'result-file-header'};

printf FILE ("%-s %-s %-s %s\n","SpectrumIndex","TotalIonCount","Spectrum","Duration");
for my $data (@$results) {
    my $spectrum=$data->{spectrum};
    for my $data1 (@$results1){    
    printf FILE ("%-s %-s %-s %-s\n",$data->{"spectrum-index"}, $data->{tic}, $spectrum          
->{'content'},$data1->{duration});
    }   
  }

It gives the following output to the text file:

 SpectrumIndex TotalIonCount Spectrum Duration
 Integer Float mass,abundance;mass1,abundance1;
                 mass2,abundance2;mass6,abundance6 Float
 Integer Float mass3,abundance3;mass4,abundance4;
                 mass5,abundance5 Float

Any help is appreciated!

Upvotes: 0

Views: 197

Answers (3)

7stud
7stud

Reputation: 48589

  1. In modern perl:

    • you use the three argument form of open()
    • you use my variables instead of bareword filehandles
    • and you output the system error message ($!) when things go wrong:

    open my $INFILE, '<', $fname
    or die "Couldn't open $fname: $!";

  2. You have to print line by line. You can't print one column and then another column.
    So when you do this:

    printf FILE (
    "%-s %-s %-s %-s\n",
    $data->{"spectrum-index"},
    $data->{tic},
    $spectrum->{'content'},
    $data1->{duration}
);

    ... then of course all that data is going to be on one line.

Upvotes: 0

B.Hall
B.Hall

Reputation: 25

i figured it out...i just used: 

my $content=$spectrum->{'content'};
$content=~s/\s+$//g

and that did the trick

Upvotes: 0

user2461880
user2461880

Reputation: 161

Just put how many character you want in the printf: e.g.

printf FILE ("%20s %20s %40s %10s\n",...)

Upvotes: 1

Related Questions