FishMonger
Veteran
Nov 13, 2012, 7:10 PM
Post #22 of 31
(8817 views)
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Re: [MB123] File parsing problem, Use of uninitialised value error.
[In reply to]
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I've been following this thread but until now I've not contributed.
So far, the helpers have indirectly stated that you first need to correct the issues with the input before you can parse the data correctly. While that might be the ideal approach, it is not always/often possible. Instead, I suggest that you add additional/different error checking to accommodate the problems.
Here's my test script, which has the minimal level of error checking that I think it might need, but in a production level script, the error checking/handing would be expanded.
In this example I'm putting the input data inside the the script but also include commented out lines that read the input data from an external file.
#!/usr/bin/perl
use strict;
use warnings;
use Carp;
my %cod = (
1 => "Int",
2 => "non",
3 => "syn",
4 => "stop",
);
my $input_file = 'BSAC.txt';
my $output_file = 'output.txt';
#open my $input_fh, '<', $input_file or croak "could not open '$input_file' <$!>\n";
open my $output_fh, '>', $output_file or croak "could not open '$output_file <$!>\n";
printf {$output_fh} ("%-12s %-15s %-10s\n", 'Coordinate', 'No of Strains', 'AA Change');
print {$output_fh} '-' x 38, "\n";
RECORD:
#while (my $line = <$input_fh>) {
while (my $line = <DATA>) {
chomp $line;
if ( $line =~ /^FT \s+ SNP \s+ (\d+)/x) {
my $snp = $1;
#my $note = <$input_fh>;
my $note = <DATA>;
if ( $note =~ /^FT \s+ \/note = "(.+)"/x ) {
$note = $1;
}
else {
carp qq(format error parsing "note" at or near line $. - skipping this record\n);
next RECORD;
}
my $count = ($note =~ tr/=/=/) || 0;
my ($change) = $note =~ /\(AA ([^)]+)\) \s+$/x ? $1 : '';
#my $colour = <$input_fh>;
my $colour = <DATA>;
$colour or do {
carp qq(format error parsing "colour" at or near line $. - skipping this record\n);
next RECORD;
};
if ( $colour =~ /^FT \s+ \/colour = (\d+)/x ) {
$colour = $1;
}
else {
carp qq(format error parsing "colour" at or near line $. - skipping this record\n);
next RECORD;
}
if ($cod{$colour} eq 'non') {
printf {$output_fh} ("%-12s %-14d %-10s\n", $snp, $count, $change);
}
}
}
#close $input_fh;
close $output_fh;
__DATA__
FT SNP 27534
FT /note="refAllele: T SNPstrains: 7564_8#80=C (non-synonymous) (AA Leu->Ser) "
FT /colour=2
FT SNP 27682
FT /note="refAllele: T SNPstrains: 7414_8#37=C (synonymous) "
FT /colour=3
FT SNP 27710
FT /note="refAllele: G SNPstrains: 7083_1#32=T (non-synonymous) (AA Val->Phe) 7521_5#41=T (non-synonymous) (AA Val->Phe) "
FT /colour=2
FT SNP 27771
FT /note="refAllele: A SNPstrains: 7480_8#28=G (non-synonymous) (AA His->Arg) "
FT /colour=2
FT SNP 28047
FT /note="refAllele: A SNPstrains: 7480_7#86=T (non-synonymous) (AA Lys->Ile) "
FT /colour=2
FT SNP 28490
FT /note="refAllele: G SNPstrains: 7083_1#4=T (non-synonymous) (AA Gly->Cys) 7554_6#38=T (non-synonymous) (AA Gly->Cys) "
FT SNP 28492
FT /note="refAllele: C SNPstrains: 7414_7#66=A (synonymous) 7414_8#44=A (synonymous) 7521_6#54=A (synonymous) "
FT /colour=3
FT SNP 28548
FT /note="refAllele: C SNPstrains: 7414_8#65=T (non-synonymous) (AA Ser->Leu) "
FT /colour=2
FT SNP 28787
FT /note="refAllele: G SNPstrains: 7414_7#14=A (non-synonymous) (AA Asp->Asn) "
FT /colour=2
FT SNP 28840
FT /note="refAllele: C SNPstrains: 7414_8#51=T (synonymous) 7414_8#71=T (synonymous) "
FT /colour=3
FT SNP 28941
FT /note="refAllele: A SNPstrains: 7083_1#1=G (non-synonymous) (AA Gln->Arg) "
FT /colour=2
FT SNP 29080
FT /note="refAllele: A SNPstrains: 7414_7#49=G (synonymous) 7521_6#39=G (synonymous) 7564_8#91=G (synonymous) 7712_8#14=G (synonymous) "
FT /colour=3
FT SNP 29214
FT /note="refAllele: T SNPstrains: 7554_6#36=C (non-synonymous) (AA Val->Ala) "
FT /colour=2
FT SNP 29574
FT /note="refAllele: C SNPstrains: 7065_8#73=T (non-synonymous) (AA Pro->Leu) "
FT /colour=2
FT SNP 29610
FT /note="refAllele: C SNPstrains: 7480_8#12=T "
FT /colour=1
FT SNP 29658
FT /note="refAllele: T SNPstrains: 7564_8#79=A "
Based on the sample input data, this is the contents of output.txt.
Coordinate No of Strains AA Change
--------------------------------------
27534 1 Leu->Ser
27710 2 Val->Phe
27771 1 His->Arg
28047 1 Lys->Ile
28548 1 Ser->Leu
28787 1 Asp->Asn
28941 1 Gln->Arg
29214 1 Val->Ala
29574 1 Pro->Leu
And here are the "error" messages sent to stderr, which I might direct to an "error" file for later review.
format error parsing "colour" at or near line 19 - skipping this record
at D:\test\Perl-1.pl line 54, <DATA> line 19.
format error parsing "colour" at or near line 48 - skipping this record
at D:\test\Perl-1.pl line 46, <DATA> line 48. |
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