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#1: don"t know where to start??? comparing files

Posted on 2011-10-12 16:01:15 by Natalie Conte

HI All,
I have 2 sets of files I want to compare,and I don't know where to start
to get what I want :(
I have a reference file ( see ref for example) with a chromosome name, a
start and a end position
Chr7 115249090 115859515
Chr8 25255496 29565459
Chr13 198276698 298299815
ChrX 109100951 109130998


and I have a file (file_test) file I want to parse against this
reference ref.txt
Chr1 115249098
Chr1 1362705
Chr8 25255996
Chr8 1362714
Chr1 1362735
ChrX 109100997

So if the position on the file_test is found in ref_file it is kept in a
new file, if not discarded.

I am looking for advises /modules I could use to compare those 2 files .
many thanks in advance for any tips
Nat


--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

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#2: Re: don"t know where to start??? comparing files

Posted on 2011-10-12 16:32:16 by Shlomi Fish

Hi Nathalie,

On Wed, 12 Oct 2011 15:01:15 +0100
Nathalie Conte <nac@sanger.ac.uk> wrote:

> HI All,
> I have 2 sets of files I want to compare,and I don't know where to start
> to get what I want :(
> I have a reference file ( see ref for example) with a chromosome name, a
> start and a end position
> Chr7 115249090 115859515
> Chr8 25255496 29565459
> Chr13 198276698 298299815
> ChrX 109100951 109130998
>
>
> and I have a file (file_test) file I want to parse against this
> reference ref.txt
> Chr1 115249098
> Chr1 1362705
> Chr8 25255996
> Chr8 1362714
> Chr1 1362735
> ChrX 109100997
>
> So if the position on the file_test is found in ref_file it is kept in a
> new file, if not discarded.

What I would do is construct a large array of the ranges where the indices can
be found (using start/end), while merging overlapping ranges, and then sort it
to have a sorted array of ([$start1,$end1],[$start2, $end2]...) ranges.

Then I will lookup these points in the array using binary search:

* http://search.cpan.org/dist/Search-Binary/

* http://search.cpan.org/~stevan/Tree-Binary-0.07/lib/Tree/Bin ary/Search.pm#OTHER_TREE_MODULES

Regards,

Shlomi Fish

>
> I am looking for advises /modules I could use to compare those 2 files .
> many thanks in advance for any tips
> Nat
>
>



--
------------------------------------------------------------ -----
Shlomi Fish http://www.shlomifish.org/
Stop Using MSIE - http://www.shlomifish.org/no-ie/

Larry Wall is lazy, impatient and full of hubris.

Please reply to list if it's a mailing list post - http://shlom.in/reply .

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#3: Re: don"t know where to start??? comparing files

Posted on 2011-10-12 17:17:52 by Shawn H Corey

On 11-10-12 10:01 AM, Nathalie Conte wrote:
> HI All,
> I have 2 sets of files I want to compare,and I don't know where to start
> to get what I want :(
> I have a reference file ( see ref for example) with a chromosome name, a
> start and a end position
> Chr7 115249090 115859515
> Chr8 25255496 29565459
> Chr13 198276698 298299815
> ChrX 109100951 109130998
>
>
> and I have a file (file_test) file I want to parse against this
> reference ref.txt
> Chr1 115249098 Chr1 1362705 Chr8 25255996 Chr8 1362714 Chr1 1362735 ChrX
> 109100997
> So if the position on the file_test is found in ref_file it is kept in a
> new file, if not discarded.
>
> I am looking for advises /modules I could use to compare those 2 files .
> many thanks in advance for any tips
> Nat
>
>

Try:

#!/usr/bin/env perl

use strict;
use warnings;

# file names; change as needed
my $ref_file = 'ref.txt';
my $data_file = 'test.txt';

# a hash for hold the start and end positions from the ref file
my %ref = ();

# main
load_ref();
scan();

# load the ref file into %ref
sub load_ref {

open my $ref_fh, '<', $ref_file or die "could not open $ref_file: $!\n";

while( my $line = <$ref_fh> ){

# extract the items from the line
my ( $id, $start, $end ) = split ' ', $line;

# store as HoH
$ref{$id} = {
start => $start,
end => $end,
};
}

close $ref_fh;
}

sub scan {

open my $data_fh, '<', $data_file or die "could not open $data_file:
$!\n";

while( my $line = <$data_fh> ){

# extract each pair of IDs and numbers
while( $line =~ m{ \s* (\S+) \s* (\S+) }gmsx ){
my $id = $1;
my $number = $2;

# see if the number is between the start and end
if( exists $ref{$id}
&& $ref{$id}{start} <= $number
&& $number <= $ref{$id}{end}
){
printf "%-7s % 15s\n", $id, $number;
}
}
}
close $data_fh;
}

__END__

--
Just my 0.00000002 million dollars worth,
Shawn

Confusion is the first step of understanding.

Programming is as much about organization and communication
as it is about coding.

The secret to great software: Fail early & often.

Eliminate software piracy: use only FLOSS.

"Make something worthwhile." -- Dear Hunter

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#4: Re: don"t know where to start??? comparing files

Posted on 2011-10-13 04:07:58 by merlyn

>>>>> "Shawn" == Shawn H Corey <shawnhcorey@gmail.com> writes:

Shawn> #!/usr/bin/env perl

Please. Don't.

--
Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095
<merlyn@stonehenge.com> <URL:http://www.stonehenge.com/merlyn/>
Smalltalk/Perl/Unix consulting, Technical writing, Comedy, etc. etc.
See http://methodsandmessages.posterous.com/ for Smalltalk discussion

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#5: Re: don"t know where to start??? comparing files

Posted on 2011-10-13 13:34:19 by dermot

On 13 October 2011 03:07, Randal L. Schwartz <merlyn@stonehenge.com> wrote:
>>>>>> "Shawn" == Shawn H Corey <shawnhcorey@gmail.com> writes:
>
> Shawn> #!/usr/bin/env perl
>
> Please. =A0Don't.

This is quite relevant for me at the moment. I have a couple of
projects where I will not be using the system perl and I was under
the impression that using `env perl` was the preferred method. So it
you using perlbrew, local::lib or just build a perl in some exotic
directory, are you suggested we give the path to the perl you want to
use? What's the reasoning?
Thanks,
Dermot

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#6: Re: don"t know where to start??? comparing files

Posted on 2011-10-13 15:43:32 by Igor Dovgiy

--0016e65a076e99894804af2e5369
Content-Type: text/plain; charset=ISO-8859-1

May be this'll help? )


#!/usr/bin/perl
use strict;
use warnings;
die 'Usage: ' . __FILE__ . " file1[ file2...]\n" unless @ARGV;

my $ref_file = 'ref.txt';
my $new_file = 'new.txt';

open my $ref_fh, '<', $ref_file
or die "Failed to open reference file - $!\n";
my %limits_for;
while (<$ref_fh>) {
next unless /\d/; # skipping infoless lines
my ($chromosome, $start, $end) = split;
$limits_for{ $chromosome } = {
start => $start,
end => $end,
};
}
close $ref_fh;

my %positions_for;
while (<>) {
my ($chromosome, $pos) = split;
push @{ $positions_for{ $chromosome } }, $pos;
}

my %in_limits_for;
foreach my $chromosome (keys %positions_for) {
next unless exists $limits_for{ $chromosome };
my @in_limits = grep {
$limits_for{ $chromosome }->{start} <= $_
&&
$_ <= $limits_for{ $chromosome }->{end}
} @{ $positions_for{ $chromosome } };
$in_limits_for{ $chromosome } = \@in_limits;
}

open my $new_fh, '>', $new_file
or die "Failed to write out results - $!\n";
foreach my $chromosome (keys %in_limits_for) {
foreach my $pos ( @{ $in_limits_for{ $chromosome } } ) {
printf $new_fh
"%-7s %15s\n", $chromosome, $pos;
}
print $new_fh '=' x 80 . "\n";
}
close $new_fh;

-- iD

2011/10/12 Nathalie Conte <nac@sanger.ac.uk>

> HI All,
> I have 2 sets of files I want to compare,and I don't know where to start to
> get what I want :(
> I have a reference file ( see ref for example) with a chromosome name, a
> start and a end position
> Chr7 115249090 115859515
> Chr8 25255496 29565459
> Chr13 198276698 298299815
> ChrX 109100951 109130998
>
>
> and I have a file (file_test) file I want to parse against this reference
> ref.txt
> Chr1 115249098 Chr1 1362705 Chr8 25255996 Chr8 1362714 Chr1
> 1362735 ChrX 109100997
> So if the position on the file_test is found in ref_file it is kept in a
> new file, if not discarded.
>
> I am looking for advises /modules I could use to compare those 2 files .
> many thanks in advance for any tips
> Nat
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
> a charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
> --
> To unsubscribe, e-mail: beginners-unsubscribe@perl.org
> For additional commands, e-mail: beginners-help@perl.org
> http://learn.perl.org/
>
>
>

--0016e65a076e99894804af2e5369--

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#7: Re: don"t know where to start??? comparing files

Posted on 2011-10-14 08:08:46 by merlyn

>>>>> "Dermot" == Dermot <paikkos@gmail.com> writes:

Dermot> On 13 October 2011 03:07, Randal L. Schwartz <merlyn@stonehenge.c=
om> wrote:
>>>>>>> "Shawn" == Shawn H Corey <shawnhcorey@gmail.com> writes:
>>=20
Shawn> #!/usr/bin/env perl
>>=20
>> Please. àDon't.

Dermot> This is quite relevant for me at the moment. I have a couple of
Dermot> projects where I will not be using the system perl and I was und=
er
Dermot> the impression that using `env perl` was the preferred method. So=
it
Dermot> you using perlbrew, local::lib or just build a perl in some exoti=
c
Dermot> directory, are you suggested we give the path to the perl you wan=
t to
Dermot> use? What's the reasoning?

Because this uses *my* environment when I run *your* Perl script.
That's broken.

Hardcode the path. Or install it using any of the module tools, which
will replace #!perl with the proper hardcoded local Perl path.

--=20
Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 00=
95
<merlyn@stonehenge.com> <URL:http://www.stonehenge.com/merlyn/>
Smalltalk/Perl/Unix consulting, Technical writing, Comedy, etc. etc.
See http://methodsandmessages.posterous.com/ for Smalltalk discussion

--=20
To unsubscribe, e-mail: beginners-unsubscribe@perl.org
For additional commands, e-mail: beginners-help@perl.org
http://learn.perl.org/

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#8: Re: don"t know where to start??? comparing files

Posted on 2011-10-14 15:50:33 by Shawn H Corey

On 11-10-14 02:08 AM, Randal L. Schwartz wrote:
> Because this uses*my* environment when I run*your* Perl script.
> That's broken.

Then you should un-break your environment. I can help you if you're
using Linux. If you're using Windows, I'm sure there are many on the
list who can help.


--
Just my 0.00000002 million dollars worth,
Shawn

Confusion is the first step of understanding.

Programming is as much about organization and communication
as it is about coding.

The secret to great software: Fail early & often.

Eliminate software piracy: use only FLOSS.

"Make something worthwhile." -- Dear Hunter

--
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For additional commands, e-mail: beginners-help@perl.org
http://learn.perl.org/

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#9: Deployment Issues (Was: don"t know where to start??? comparingfiles)

Posted on 2011-10-14 17:05:45 by RWeidner

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#10: Re: don"t know where to start??? comparing files

Posted on 2011-10-18 16:13:00 by merlyn

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#11: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 16:20:24 by j.madrigal2

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#12: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 16:26:55 by Rob Coops

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#13: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 16:30:33 by merlyn

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#14: Re: don"t know where to start??? comparing files

Posted on 2011-10-18 16:33:37 by Zachary Zebrowski

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#15: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 17:05:14 by j.madrigal2

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#16: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 17:17:30 by Ryan Munson

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#17: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 17:22:31 by j.madrigal2

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#18: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 17:32:49 by Phil Dobbin

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#19: Re: Installing CPAN Params::Validate and DateTime on Mac OS X 10.6.8

Posted on 2011-10-18 20:56:51 by j.madrigal2

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