in reply to Getting data from a file (Operons and Genes).

chrisantha, try this:

#!/perl/bin/perl -w
use strict;
use Data::Dumper;

my $hash = {};
for (<DATA>) {
  chomp;
  my @fields = split(/\s{4}/, $_);
  my @genes  = split(',', $fields[3]);
  @genes = map { (split('\|'))[1] } @genes;
  push(@{$hash->{$fields[0]}}, \@genes);
}
print Dumper($hash);

__DATA__
malS    1    forward    malS|b3571,
malT    1    forward    malT|b3418,
malXY    2    forward    malX|b1621,malY|b1622,
malZ    1    forward    malZ|b0403,
manA    1    forward    manA|b1613,

__OUTPUT__
$VAR1 = {
          'malZ' => [
                      [
                        'b0403'
                      ]
                    ],
          'malS' => [
                      [
                        'b3571'
                      ]
                    ],
          'manA' => [
                      [
                        'b1613'
                      ]
                    ],
          'malXY' => [
                       [
                         'b1621',
                         'b1622'
                       ]
                     ],
          'malT' => [
                      [
                        'b3418'
                      ]
                    ]
        };

[download]

Is this what you're looking for?

Updated: Added __OUTPUT__


Where do you want *them* to go today?

Replies are listed 'Best First'.
Re^2: Getting data from a file (Operons and Genes).
by ysth (Canon) on Jun 14, 2007 at 22:56 UTC
    You've got an unnecessary level of array reference there; you could remove it by changing 
    push(@{$hash->{$fields[0]}}, \@genes);

    [download]
    to 
    push(@{$hash->{$fields[0]}}, @genes);

    [download]
    giving output: 
    $VAR1 = {
          'malZ' => [
                      'b0403'
                    ],
          'malS' => [
                      'b3571'
                    ],
          'manA' => [
                      'b1613'
                    ],
          'malXY' => [
                       'b1621',
                       'b1622'
                     ],
          'malT' => [
                      'b3418'
                    ]
        };

    [download]
[reply]
[d/l]
[select]

      I chose not to assume that an operon was unique thoughout the file, since it wasn't explicitly stated in the spec.

      If I can assume uniqueness, then I'd remove the push and change to a HoA:

      $hash->{$fields[0]} = \@genes;

      [download]

      Where do you want *them* to go today?
[reply]
[d/l]
        Thanks, I was trying this but failing. 
        
#!/usr/bin/perl


use strict;

my $operon; 
my %operonHash; 


while (<>) { 

chomp; 
if ( /(\b.+?\b)/ ) { # word boundary + any character at least once, up
+ to the first word boundary. 
    #print "Matched: |$`<$&?>$'|\n"; 
    $operon = $_; 
    #print  $& . " " ; 
    $operonHash{$&} = ();  
    } else { 
    print "No match. \n";
    }
    
    print "\n"; 
    
if ( /\w+\|/ ) { # word boundary + any character at least once, up to 
+the first word boundary. 
    print "Matched: |$`<<$&>>$'|\n"; 

    } else { 
    print "No match. \n";
    }

}

        [download]
        #The problem is, 1. How to get rid of the | from the expression that was found, and 2. How to get MULTIPLE genes before | when more than one gene appears on a line?
[reply]
[d/l]
      Thanks again. I tried your code on this data 
       

C0067    1    forward    C0067|,
C0293    1    forward    C0293|,
C0343-dbpA    2    forward    C0343|,dbpA|b1343,
C0465    1    forward    C0465|,
C0614    1    reverse    C0614|,
C0719    1    forward    C0719|,
IS128    1    forward    IS128|,
aaeR    1    forward    aaeR|b3243,
aaeXAB    3    reverse    aaeA|b3241,aaeB|b3240,aaeX|b3242,
aas-ygeD    2    reverse    aas|b2836,ygeD|b2835,
aat    1    reverse    aat|b0885,
abgABT-ogt    4    reverse    abgA|b1338,abgB|b1337,abgT|b1336,ogt|b13
+35,
abgR    1    forward    abgR|b1339,
abrB    1    reverse    abrB|b0715,
accA    1    forward    accA|b0185,
accBC    2    forward    accB|b3255,accC|b3256,
accD    1    reverse    accD|b2316,
aceBAK    3    forward    aceA|b4015,aceB|b4014,aceK|b4016,
ackA-pta    2    forward    ackA|b2296,pta|b2297,
acnA    1    forward    acnA|b1276,
acnB    1    forward    acnB|b0118,
acpH    1    reverse    acpH|b0404,
acpT    1    forward    acpT|b3475,
acrAB    2    reverse    acrA|b0463,acrB|b0462,
acrD    1    forward    acrD|b2470,
acrEF    2    forward    acrE|b3265,acrF|b3266,
acrR    1    forward    acrR|b0464,
acs-yjcH-actP    3    reverse    acs|b4069,actP|b4067,yjcH|b4068,
ada-alkB    2    reverse    ada|b2213,alkB|b2212,
add    1    forward    add|b1623,
ade    1    forward    ade|b3665,
adhE    1    reverse    adhE|b1241,
adhP    1    reverse    adhP|b1478,
adiA    1    reverse    adiA|b4117,
adiC    1    reverse    adiC|b4115,
adiY    1    reverse    adiY|b4116,
adk    1    forward    adk|b0474,
adrA    1    forward    adrA|b0385,
aegA    1    reverse    aegA|b2468,
aer    1    reverse    aer|b3072,
aes    1    reverse    aes|b0476,
agaR    1    reverse    agaR|b3131,
agaS-kbaY-agaBCDI    6    forward    agaB|b3138,agaC|b3139,agaD|b3140,
+agaI|b3141,agaS|b3136,kbaY|b3137,
malS    1    forward    malS|b3571,
malT    1    forward    malT|b3418,
malXY    2    forward    malX|b1621,malY|b1622,
malZ    1    forward    malZ|b0403,
manA    1    forward    manA|b1613,


which gives output 


$VAR1 = {
          'malZ' => [
                      [
                        'b0403'
                      ]
                    ],
' => [    'ada-alkB     2       reverse ada|b2213,alkB|b2212,
                                                           []
                                                         ],
          'malS' => [
                      [
                        'b3571'
                      ]
                    ],
' => [    'acnA 1       forward acnA|b1276,
                                             []
                                           ],
' => [    'aegA 1       reverse aegA|b2468,
                                             []
                                           ],
' => [    'adhP 1       reverse adhP|b1478,
                                             []
                                           ],
' => [    'abgABT-ogt   4       reverse abgA|b1338,abgB|b1337,abgT|b13
+36,ogt|b1335,
                                                                      
+             []
                                                                      
+           ],
' => [    'acnB 1       forward acnB|b0118,
                                             []
                                           ],
' => [    'acpT 1       forward acpT|b3475,
                                             []
                                           ],
' => [    'ade  1       forward ade|b3665,
                                           []
                                         ],
' => [    'acrD 1       forward acrD|b2470,
                                             []
                                           ],
' => [    'acpH 1       reverse acpH|b0404,
                                             []
                                           ],
' => [    'agaR 1       reverse agaR|b3131,
                                             []
                                           ],
' => [    'C0293        1       forward C0293|,
                                          []
                                        ],
          'malXY' => [
                       [
                         'b1621',
                         'b1622'
                       ]
                     ],
' => [    'aaeR 1       forward aaeR|b3243,
                                             []
                                           ],
' => [    'ackA-pta     2       forward ackA|b2296,pta|b2297,
                                                           []
                                                         ],
' => [    'aceBAK       3       forward aceA|b4015,aceB|b4014,aceK|b40
+16,
                                                                     [
+]
                                                                   ],
' => [    'aat  1       reverse aat|b0885,
                                           []
                                         ],
' => [    'acrR 1       forward acrR|b0464,
                                             []
                                           ],
' => [    'accA 1       forward accA|b0185,
                                             []
                                           ],
' => [    'IS128        1       forward IS128|,
                                          []
                                        ],
' => [    'aaeXAB       3       reverse aaeA|b3241,aaeB|b3240,aaeX|b32
+42,
                                                                     [
+]
                                                                   ],
          'malT' => [
                      [
                        'b3418'
                      ]
                    ],
' => [    'abrB 1       reverse abrB|b0715,
                                             []
                                           ],
' => [    'C0465        1       forward C0465|,
                                          []
                                        ],
' => [    'aas-ygeD     2       reverse aas|b2836,ygeD|b2835,
                                                           []
                                                         ],
' => [    'C0614        1       reverse C0614|,
                                          []
                                        ],
' => [    'adk  1       forward adk|b0474,
                                           []
                                         ],
          'agaS-kbaY-agaBCDI    6       forward agaB|b3138,agaC|b3139,
+agaD|b3140,agaI|b3141,agaS|b3136,kbaY|b3137,' => [
                                                                      
+                                          []
                                                                      
+                                        ],
' => [    'adiC 1       reverse adiC|b4115,
                                             []
                                           ],
' => [    'aes  1       reverse aes|b0476,
                                           []
                                         ],
' => [    'accBC        2       forward accB|b3255,accC|b3256,
                                                         []
                                                       ],
' => [    'add  1       forward add|b1623,
                                           []
                                         ],
' => [    'accD 1       reverse accD|b2316,
                                             []
                                           ],
' => [    'adrA 1       forward adrA|b0385,
                                             []
                                           ],
' => [    'adiA 1       reverse adiA|b4117,
                                             []
                                           ],
' => [    'aer  1       reverse aer|b3072,
                                           []
                                         ],
' => [    'acrEF        2       forward acrE|b3265,acrF|b3266,
                                                         []
                                                       ],
' => [    'acs-yjcH-actP        3       reverse acs|b4069,actP|b4067,y
+jcH|b4068,
                                                                      
+     []
                                                                      
+   ],
' => [    'abgR 1       forward abgR|b1339,
                                             []
                                           ],
' => [    'C0719        1       forward C0719|,
                                          []
                                        ],
' => [    'adiY 1       reverse adiY|b4116,
                                             []
                                           ],
' => [    'C0343-dbpA   2       forward C0343|,dbpA|b1343,
                                                          []
                                                        ],
          'manA' => [
                      [
                        'b1613'
                      ]
                    ],
' => [    'acrAB        2       reverse acrA|b0463,acrB|b0462,
                                                         []
                                                       ],
' => [    'C0067        1       forward C0067|,
                                          []
                                        ],
' => [    'adhE 1       reverse adhE|b1241,
                                             []
                                           ]
        };

      [download]
      Which is strange because it works for the example data you sent me which I cut and pasted into the above data, but not for the original data file. Please can you explain this? Yours, Chrisantha
[reply]
[d/l]
        I think you have tabs separating the fields instead of 4 spaces that the code somebody wrote is expecting, and unexpected carriage return characters at the end of lines. Changing it to 
        my @fields = split(' ', $_);

        [download]
        (or just my @fields = split;, since ' ' and $_ are what split defaults to) solves both problems.
[reply]
[d/l]
[select]
Re^2: Getting data from a file (Operons and Genes).
by chrisantha (Initiate) on Jun 14, 2007 at 23:50 UTC
    Yes, thanks, I was trying somethign like this and failing. <code> #!/usr/bin/perl use strict; my $operon; my %operonHash; while (<>) { chomp; if ( /(\b.+?\b)/ ) { # word boundary + any character at least once, up to the first word boundary. #print "Matched: |$`<$&?>$'|\n"; $operon = $_; #print $& . " " ; $operonHash{$&} = (); } else { print "No match. \n"; } print "\n"; if ( /\w+\|/ ) { # word boundary + any character at least once, up to the first word boundary. print "Matched: |$`<<$&>>$'|\n"; } else { print "No match. \n"; } } <\code> #The problem is, 1. How to get rid of the | from the expression that was found, and 2. How to get MULTIPLE genes before | when more than one gene appears on a line?
[reply]

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