Help: Odd Output

[Amy Lee]

Hello,

I wrote a script to check the location. Here's my codes.

#!/usr/bin/perl -w

use warnings;
use strict;

my $location = $ARGV[0];
open my $LOCATION, '<', "$location";

my @stack;
while (<$LOCATION>)
{
chomp;
my $raw_seq_id = (split /\s+/)[0];
my $mature_start = (split /\s+/)[1];
my $mature_end = (split /\s+/)[2];
my $mature_id = (split /_/, $raw_seq_id)[3];
my $i;
my $num = 0;
open my $CT, '<', "$raw_seq_id"."\.ct";
while (<$CT>)
{
if ((?dG? ... /dG/) && (!/dG/))
{
push @stack, (split /\s+/)[4];
}
}
for ($i = $mature_start - 1;$i < $mature_end;$i++)
{
if ($stack[$i] == 0)
{
$num = $num + 1;
}
else
{
next;
}
}
if ($num <= 2)
{
print "$raw_seq_id $num\n";
}
else
{
next;
}
}

And this script will read the data, the first column is the sequence tag,
the second column is start position, the third column is end position.
Here's the sample data.

Gm17_37759439_37759542_ath-MIR156c 12 31
.... ... ... ...

Then, read the first column, there's a file called
Gm17_37759439_37759542_ath-MIR156c.ct,

Here's the CT format data.

1 U 0 2 0 1 0 0
2 G 1 3 0 2 0 0
3 G 2 4 0 3 0 4
4 A 3 5 102 4 3 5
5 C 4 6 101 5 4 6
6 A 5 7 100 6 5 0
7 G 6 8 97 7 0 8
8 A 7 9 96 8 7 9
9 A 8 10 95 9 8 10
10 A 9 11 94 10 9 0
11 U 10 12 0 11 0 0
12 U 11 13 0 12 0 0
13 G 12 14 91 13 0 14
14 A 13 15 90 14 13 15
15 C 14 16 89 15 14 16
16 A 15 17 88 16 15 17
17 G 16 18 0 17 16 18
18 A 17 19 85 18 17 19
19 A 18 20 0 19 18 20
20 G 19 21 83 20 19 21
21 A 20 22 82 21 20 22
22 G 21 23 0 22 21 23
23 A 22 24 79 23 22 24
24 G 23 25 78 24 23 25
25 U 24 26 0 25 24 26
26 G 25 27 76 26 25 27
27 A 26 28 0 27 26 28
28 G 27 29 74 28 27 29
29 C 28 30 73 29 28 30
30 A 29 31 72 30 29 31
31 C 30 32 0 31 30 32
32 A 31 33 0 32 31 0
33 A 32 34 0 33 0 0
34 A 33 35 68 34 0 35
35 G 34 36 67 35 34 36
36 A 35 37 66 36 35 37
37 G 36 38 65 37 36 38
38 G 37 39 64 38 37 39
39 C 38 40 63 39 38 40
40 A 39 41 62 40 39 0
41 C 40 42 0 41 0 0
42 U 41 43 0 42 0 0
43 U 42 44 60 43 0 44
44 G 43 45 59 44 43 45
45 A 44 46 58 45 44 46
46 U 45 47 57 46 45 47
47 A 46 48 56 47 46 48
48 U 47 49 55 48 47 49
49 A 48 50 54 49 48 0
50 A 49 51 0 50 0 0
51 A 50 52 0 51 0 0
52 U 51 53 0 52 0 0
53 C 52 54 0 53 0 0
54 U 53 55 49 54 0 55
55 A 54 56 48 55 54 56
56 U 55 57 47 56 55 57
57 A 56 58 46 57 56 58
58 U 57 59 45 58 57 59
59 C 58 60 44 59 58 60
60 A 59 61 43 60 59 0
61 C 60 62 0 61 0 0
62 U 61 63 40 62 0 63
63 G 62 64 39 63 62 64

According to the CT file, the fifth column is what I will process, read
the start position to the end position from sample data, then get the same
position from the fifth column. If at this range(start - end) contains
less than 2 zeros, will print the proper sequences tag and the number of
zero.

However, when I run my script, just print sequences tag and the number 2.
Actually, my code should print nothing because this isn't fit in the
condition I write.

So could anyone show me the hints? Thank you very much.

Best Regards,

Amy Lee

 

[Amy Lee]

And further, I wonder that my codes structure has serious problem, when
sample data has many items it will failed and output odd output.

Thank you for help.

Amy

 

[Tad J McClellan]

open my $LOCATION, '<', "$location";

^ ^
^ ^

You should not quote lone variables:

perldoc -q vars

What's wrong with always quoting "$vars"?


You should always, yes *always*, check the return value from open():

open my $LOCATION, '<', $location or die "could not open '$location' $!";

my $raw_seq_id = (split /\s+/)[0];
my $mature_start = (split /\s+/)[1];
my $mature_end = (split /\s+/)[2];

my($raw_seq_id, $mature_start, $mature_end) = split /\s+/;

open my $CT, '<', "$raw_seq_id"."\.ct";

open my $CT, '<', "$raw_seq_id.ct" or die ...;

 

[Amy Lee]

Thank you all, I have solved such problem. My problem is the @stack
dose not refresh when go to next while loop.

Best Regards,

Amy

 

[John W. Krahn]

Hello,

I wrote a script to check the location. Here's my codes.

#!/usr/bin/perl -w

use warnings;
use strict;

my $location = $ARGV[0];
open my $LOCATION, '<', "$location";

my @stack;
while (<$LOCATION>)
{
chomp;
my $raw_seq_id = (split /\s+/)[0];
my $mature_start = (split /\s+/)[1];
my $mature_end = (split /\s+/)[2];
my $mature_id = (split /_/, $raw_seq_id)[3];
my $i;
my $num = 0;
open my $CT, '<', "$raw_seq_id"."\.ct";
while (<$CT>)
{
if ((?dG? ... /dG/) && (!/dG/))
{
push @stack, (split /\s+/)[4];
}
}
for ($i = $mature_start - 1;$i < $mature_end;$i++)
{
if ($stack[$i] == 0)
{
$num = $num + 1;
}
else
{
next;
}
}
if ($num <= 2)
{
print "$raw_seq_id $num\n";
}
else
{
next;
}
}

You can simplify that a bit to:

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

@ARGV == 1 or die "Usage: $0 FILENAME\n";

my $location = $ARGV[ 0 ];
open my $LOCATION, '<', $location or die "Cannot open '$location' $!";

while ( <$LOCATION> ) {
my ( $raw_seq_id, $mature_start, $mature_end ) = split;
my $mature_id = ( split /_/, $raw_seq_id )[ 3 ];

open my $CT, '<', "$raw_seq_id.ct" or die "Cannot open
'$raw_seq_id.ct' $!";

my @stack;
while ( <$CT> ) {
if ( ?dG? ... /dG/ and !/dG/ ) {
push @stack, ( split )[ 4 ];
next;
}
last if @stack;
}

if ( 2 > grep $_ == 0, @stack[ $mature_start - 1 .. $mature_end - 1
] ) {
print "$raw_seq_id $num\n";
}
}

__END__




John

 

[Dr.Ruud]

#!/usr/bin/perl -w

use warnings;
use strict;

The combination "-w" and "use warnings;" is odd.

my $location = $ARGV[0];
open my $LOCATION, '<', "$location";

open my $LOCATION, '<', $location or die $!;

my @stack;
while (<$LOCATION>)
{
chomp;
my $raw_seq_id = (split /\s+/)[0];

Replace /\s+/ by " ". Then remove it, because it is the default.

my $mature_start = (split /\s+/)[1];
my $mature_end = (split /\s+/)[2];

Alternative:

my ($raw_seq_id, $mature_start, $mature_end) = split;

my $mature_id = (split /_/, $raw_seq_id)[3];
my $i;
my $num = 0;
open my $CT, '<', "$raw_seq_id"."\.ct";

open my $CT, '<', "$raw_seq_id.ct" or die $!;

 

[Tad J McClellan]

Amy Lee wrote:

my $location = $ARGV[0];
open my $LOCATION, '<', "$location";

open my $LOCATION, '<', $location or die $!;

Amy,


When good programming practices are shown to you here, please adopt
those practices in all future posts.

Otherwise, folks will stop helping you, or get tired of repeating
the good practice over and over.

It was pointed out to you that you should check the return value
from open() back in August 2007.

Please adopt a coding style that includes always checking the
return value from open().