Hi,
I have this network file based on gene expression data that indicates interactions between genes such that the first column is the source and the second column is the target, the third column is the edge attribute for the interaction between first and second column, the fourth column is again the target of the first column and fifth column is the edge attribute for this interaction and so on...I'm trying to use this file to generate a network in cytoscape but all sources have to be in 1st column and targets have to be in 2nd column and any edge attributes thereafter. How can I convert this file into 3 columns with 1st column being source, 2nd target and 3rd the edge attribute. Can it be done in R?
A4GALT ABI1 0.290467 ABL1 0.291354 ACTC1 0.290467 AKR1B10 0.322647 AMN1 0.290467
AAGAB AHCYL1 0.286272 ALG10 0.275442 ANKRD15 0.303029 CA12 0.303029 CDC42SE2 0.286272
AARSD1 AARSD1 0.274792 ABCC4 0.27289 ACADL 0.349349 ACBD5 0.329398 ACSL4 0.335957
AARSD1 AARSD1 0.274792 ACADL 0.274792 ACBD5 0.26986 ACSL4 0.291354 ACTR3B 0.26986
Edit: The output file should look like this for example the first line should become:
A4GALT ABI1 0.290467
A4GALT ABL1 0.291354
A4GALT ACTC1 0.290467
A4GALT AKR1B10 0.322647
A4GALT AMN1 0.290467
and similarly all lines should be converted to such format in a single text file.
code edit:
#!/usr/bin/env perl
open(INFILE, "<aracne_network_microarray.txt") or die ("couldn't open the file\n");
use v5.10;
use strict;
use warnings;
my @a =();
my @b =();
open(MYOUTFILE, ">aracne_network_output.txt");
while (<INFILE>) {
chomp;
s/^\t|^\s+|//;
my ($source, $tar, $att, @f) = split;
@a = join ("\t", $source, $tar, $att);
while (my ($targ, $attr) = splice(@f, 0, 2)) {
@b = join ("\t", $source, $targ, $attr);
print MYOUTFILE "@b" }
}
close(MYOUTFILE)
Thanks alot!!!
1 answer
You could do this in R but I prefer to do these things in Perl because it is much more expressive and powerful for text processing. What I mean is that you can write out what you want to do in English:
#!/usr/bin/env perl
# pseudocode follows
read in a line of data
split the line into the component fields
say what you want (in this case, a source followed by a target, followed by the edge attribute)
repeat the previous step for each target
# end
and already you have something that is nearly ready to execute. Below you can see the real code is not very different from the plain English version:
#!/usr/bin/env perl
use v5.10;
use strict;
use warnings;
while (<DATA>) {
chomp;
s/^\t|^\s+|//;
my ($source, $tar, $att, @f) = split;
say join "\t", $source, $tar, $att;
while (my ($targ, $attr) = splice(@f, 0, 2)) {
say join "\t", $source, $targ, $attr;
}
}
__DATA__
A4GALT ABI1 0.290467 ABL1 0.291354 ACTC1 0.290467 AKR1B10 0.322647 AMN1 0.290467
AAGAB AHCYL1 0.286272 ALG10 0.275442 ANKRD15 0.303029 CA12 0.303029 CDC42SE2 0.286272
AARSD1 AARSD1 0.274792 ABCC4 0.27289 ACADL 0.349349 ACBD5 0.329398 ACSL4 0.335957
AARSD1 AARSD1 0.274792 ACADL 0.274792 ACBD5 0.26986 ACSL4 0.291354 ACTR3B 0.26986
Running this gives your source-target-attribute:
$ perl biostar75832.pl
A4GALT ABI1 0.290467
A4GALT ABL1 0.291354
A4GALT ACTC1 0.290467
A4GALT AKR1B10 0.322647
A4GALT AMN1 0.290467
AAGAB AHCYL1 0.286272
AAGAB ALG10 0.275442
AAGAB ANKRD15 0.303029
AAGAB CA12 0.303029
AAGAB CDC42SE2 0.286272
AARSD1 AARSD1 0.274792
AARSD1 ABCC4 0.27289
AARSD1 ACADL 0.349349
AARSD1 ACBD5 0.329398
AARSD1 ACSL4 0.335957
AARSD1 AARSD1 0.274792
AARSD1 ACADL 0.274792
AARSD1 ACBD5 0.26986
AARSD1 ACSL4 0.291354
AARSD1 ACTR3B 0.26986
You can load this into Cytoscape by using the Import->"as table" and then indicating what fields are the source, target, and attribute.
Hi, I'm not Noolean. A file of 3,000 lines would not really be considered "huge" by today's standards and it should only take around a second to do this (more or less). I edited the code to work with an arbitrary number of fields in this format, but please try to provide this kind of information in the future. It helps others spend less time on questions and you can get your answer faster! Hope this helps, let us know if you run into any issues.
You changed the script in your post, that is why it won't work. I modified it below to take your input as the first argument and the output as the second argument.
#!/usr/bin/env perl
use v5.10;
use strict;
use warnings;
my $usage = "perl $0 infile outfile\n";
my $infile = shift or die $usage;
my $outfile = shift or die $usage;
open my $in, '<', $infile or die "\nERROR: Could not open file $infile: $!";
open my $out, '>', $outfile or die "\nERROR: Could not open file $outfile: $!";
while (<$in>) {
chomp;
s/^\t|^\s+|//;
my ($source, $tar, $att, @f) = split;
say $out join "\t", $source, $tar, $att;
while (my ($targ, $attr) = splice(@f, 0, 2)) {
say $out join "\t", $source, $targ, $attr;
}
}
close $in;
close $out;
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I can write script for you if you could give me the example of desired output.
Ive edited the post. Thanks a lot Noolean!