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

Dear Masters,
How can I parse this text: 
__DATA__
Pm 0.2707    Minimum match (10/15)

Top 3 motifs    Wid    Score1    Segment    Con    Deg
Mtf 1    15    1.700    10    CGATATCGATTCGTT    CGATATYGAWTSSTT
Final Motif 1: Wid 15 Score1 1.700 Segment 10
         A     C     G     T     Con  rCon Deg  rDeg 
1        7    81     4     7      C    G    C    G
2       23     4    66     7      G    C    G    C
3       69    19     4     7      A    T    A    T
4        7     4     4    84      T    A    T    A
5       84     4     4     7      A    T    A    T
>2522963-2522975-reverse    St b99    CGATATCGATGGATT
>2522963-2522975-reverse    St f145    CGATATCGAATCGCT
>2522963-2522975-reverse    St b155    CGATATTAATTCCTT
>2522963-2522975-reverse    St f156    CGCTATTGAATGCGT
>2523043-2523055-reverse    St b88    CAATAGCGATTCGAT
Mtf 2    15    1.666    12    AATGAATCAATATCG    AAKSAWTYRATATCG
Final Motif 2: Wid 15 Score1 1.666 Segment 12
         A     C     G     T     Con  rCon Deg  rDeg 
1       73     4    17     6      A    T    A    T
2       60    17    17     6      A    T    A    T
3        6    17    30    46      T    A    K    M
4        6    44    44     6      C    G    S    S
5       46    17    17    20      A    T    A    T
>2522963-2522975-reverse    St b81    ACGCATTCAATAGCG
>2522963-2522975-reverse    St f82    AAGGAATTAATATCG
>2522963-2522975-reverse    St b92    AGCGATTCGATATCG
>2522963-2522975-reverse    St b106    GATGGATTTATATCT
>2522963-2522975-reverse    St f138    AATCCATCGATATCG
Mtf 3    15    1.656    10    TCGATATCGAATGGC    TCGMTATCGAWTSGC
Final Motif 3: Wid 15 Score1 1.656 Segment 10
         A     C     G     T     Con  rCon Deg  rDeg 
1        7     4     4    84      T    A    T    A
2        7    81     4     7      C    G    C    G
3       23     4    66     7      G    C    G    C
4       54    35     4     7      A    T    M    K
5        7     4     4    84      T    A    T    A
6       84     4     4     7      A    T    A    T
7        7     4    19    69      T    A    T    A
8       23    50     4    23      C    G    C    G
9       23     4    66     7      G    C    G    C
10      84     4     4     7      A    T    A    T
11      54     4     4    38      A    T    W    W
12      23     4    19    54      T    A    T    A
13       7    35    50     7      G    C    S    S
14      23    19    50     7      G    C    G    C
15      23    35    19    23      C    G    C    G
>2522963-2522975-reverse    St b87    TCAATAGCGATTCGA
>2522963-2522975-reverse    St b98    TCGATATCGATGGAT
>2522963-2522975-reverse    St f144    TCGATATCGAATCGC
>2522963-2522975-reverse    St f155    TCGCTATTGAATGCG
>2522963-2522975-reverse    St f204    TCGCTATAAAAAGGC
Total time 0:0:0.

[download]
So that it return this AoA: 
$VAR = [
['CGATATYGAWTSSTT',
 '>2522963-2522975-reverse    St f145    CGATATCGAATCGCT',
 '>2522963-2522975-reverse    St f156    CGCTATTGAATGCGT',],
['AAKSAWTYRATATCG',
 '>2522963-2522975-reverse    St f82    AAGGAATTAATATCG',
 '>2522963-2522975-reverse    St f138    AATCCATCGATATCG',],
['TCGMTATCGAWTSGC',
 '>2522963-2522975-reverse    St f144    TCGATATCGAATCGC',
 '>2522963-2522975-reverse    St f155    TCGCTATTGAATGCG',
 '>2522963-2522975-reverse    St f204    TCGCTATAAAAAGGC',]
];

[download]
Note that we: I am totally lost right from the beginning: 
use warnings;
use strict;              
use Data::Dumper;        
use Carp;

my @aoa;                 
my @temp;

while (<DATA>) {         
    chomp;               
    if (/^Mtf (\d+) (.*) ([A-Z]+)$/) { # stuck here
        print "$_ \n";            
        push @temp, ($3);
    }
    elsif (/^>(\w+) St (b|f)\d+/) { # not sure how to capture only "f"
+ here
        print "$_\n";             
    }
    push @aoa, [@temp];
}

#print Dumper \@aoa ;

[download]


---
neversaint and everlastingly indebted.......

Replies are listed 'Best First'.
Re: Selective Parsing Problem
by shmem (Chancellor) on Jun 06, 2007 at 15:49 UTC
    I'd do something like 
    #!/usr/bin/perl
use Data::Dumper;
$Data::Dumper::Indent = 1;

my $ary = [];
my $i   = -1;

while (<DATA>) {
    chomp;
    s/\r//;
    /^Mtf.*\s(\S+)$/ and push @{ $ary->[++$i] }, $1; # next array
    /\s+St f\d+/     and push @{ $ary->[$i]   }, $_;
}
print Dumper($ary);
__DATA__
- your data here -

    [download]

    Output: 

    $VAR1 = [
  [
    'CGATATYGAWTSSTT',
    '>2522963-2522975-reverse   St f145 CGATATCGAATCGCT',
    '>2522963-2522975-reverse   St f156 CGCTATTGAATGCGT'
  ],
  [
    'AAKSAWTYRATATCG',
    '>2522963-2522975-reverse   St f82  AAGGAATTAATATCG',
    '>2522963-2522975-reverse   St f138 AATCCATCGATATCG'
  ],
  [
    'TCGMTATCGAWTSGC',
    '>2522963-2522975-reverse   St f144 TCGATATCGAATCGC',
    '>2522963-2522975-reverse   St f155 TCGCTATTGAATGCG',
    '>2522963-2522975-reverse   St f204 TCGCTATAAAAAGGC'
  ]
];

    [download]

    --shmem 

    _($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}
[reply]
[d/l]
[select]

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