create a binary matrix

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

I have some files in a directory with .fq extension such as NC_002755.fq NC_009525.fq NC_009565.fq NC_012943.fq NC_016768.fq NC_016934.fq NC_017026.fq NC_017522.fq NC_017523.fq NC_017524.fq NC_017528.fq NC_018078.fq NC_018143.fq NC_020089.fq NC_020559.fq NC_021054.fq NC_021192.fq NC_021193.fq NC_021194.fq NC_021251.fq NC_021740.fq NC_022350.fq. I have created a file p.txt in the following format:


(3R)-hydroxyacyl-ACP dehydratase subunit HadA    NC_021192.1
(3R)-hydroxyacyl-ACP dehydratase subunit HadB    NC_017026.1
(dimethylallyl)adenosine tRNA methylthiotransferase    NC_009565.1    
+NC_002755.2    NC_009525.1    NC_016934.1
1,4-alpha-glucan branching protein    NC_021192.1    NC_017522.1    NC
+_016934.1    NC_018078.1    NC_020089.1    NC_002755.2    NC_017524.1
+    NC_009565.1    NC_012943.1    NC_017523.1    NC_021740.1
1,4-dihydroxy-2-naphthoate octaprenyltransferase    NC_016934.1    NC_
+017026.1    NC_009525.1
1,4-dihydroxy-2-naphthoyl-CoA synthase    NC_018143.2    NC_009565.1  
+  NC_002755.2    NC_012943.1    NC_017523.1
[download]

where NC_.... is the name of files in the directory with .fq extension. I want to create a binary matrix which has all the filenames in horizontal and genes in vertical and print 1 if filename matches else print 0. My script is :


open (FH, "p.txt");
while ($seq=<FH>)
{
@seq = split /\t/, $seq;

print @seq[0]."\t";
opendir(DIR, ".");
@files = grep(/\.fq$/,readdir(DIR));
closedir(DIR);
foreach $file (@files) {
@file1 = split /\./, $file;
$file2 = $file1[0];
$size = @files;
$file3 = $file2."\t".$file3;}
for ($i = 1; $i <= $size; $i++)
 { @seq1 = split /\./, @seq[$i];
chomp @seq1[0];
if (@seq1[0] eq $file2)
 {print "1"."\t";} 
else
 
 {print "0"."\t";}

 }
print "\n";


}
[download]

but this gives me incorrect output of 0's and 1's.

Comment on create a binary matrix Select or Download Code

Replies are listed 'Best First'.
Re: create a binary matrix by Laurent_R (Canon) on Oct 01, 2016 at 10:14 UTC
Please indent your code correctly, that would help you see some of your errors or suboptimal loops. Also use the strict and warnings pragmas, this would also help you. How about this: use strict; use warnings; my @files = qw / NC_002755.fq NC_009525.fq NC_009565.fq NC_012943.fq N +C_016768.fq NC_016934.fq NC_017026.fq NC_017522.fq NC_017523.fq NC_01 +7524.fq NC_017528.fq NC_018078.fq NC_018143.fq NC_020089.fq /; @files = map {s/\.fq$//; $_} @files; while (my $seq = <DATA>) { my @seq = split /\s+/, $seq; printf "%-50s", "@seq[0..1] "; my %found_files = map { s/\.\w+$// ; $_ => 1} grep {/NC_/} @seq[2. +.$#seq]; for my $file (@files) { print exists $found_files{$file} ? "1\t" : "0\t" } print "\n"; } __DATA__ (3R)-hydroxyacyl-ACP dehydratase subunit HadA NC_021192.1 (3R)-hydroxyacyl-ACP dehydratase subunit HadB NC_017026.1 (dimethylallyl)adenosine tRNA methylthiotransferase NC_009565.1 +NC_002755.2 NC_009525.1 NC_016934.1 1,4-alpha-glucan branching protein NC_021192.1 NC_017522.1 NC +_016934.1 NC_018078.1 NC_020089.1 NC_002755.2 NC_017524.1 + NC_009565.1 NC_012943.1 NC_017523.1 NC_021740.1 1,4-dihydroxy-2-naphthoate octaprenyltransferase NC_016934.1 NC_ +017026.1 NC_009525.1 1,4-dihydroxy-2-naphthoyl-CoA synthase NC_018143.2 NC_009565.1 + NC_002755.2 NC_012943.1 NC_017523.1 [download] Which prints this: `$ perl fq_files.pl (3R)-hydroxyacyl-ACP dehydratase 0 0 0 + 0 0 0 0 0 0 0 0 0 + 0 0 (3R)-hydroxyacyl-ACP dehydratase 0 0 0 + 0 0 0 1 0 0 0 0 0 + 0 0 (dimethylallyl)adenosine tRNA 1 1 1 + 0 0 1 0 0 0 0 0 0 + 0 0 1,4-alpha-glucan branching 1 0 1 + 1 0 1 0 1 1 1 0 1 + 0 1 1,4-dihydroxy-2-naphthoate octaprenyltransferase 0 1 0 + 0 0 1 1 0 0 0 0 0 + 0 0 1,4-dihydroxy-2-naphthoyl-CoA synthase 1 0 1 + 1 0 0 0 0 1 0 0 0 + 1 0` [download]	[reply] [d/l] [select]
Re: create a binary matrix by Random_Walk (Prior) on Oct 01, 2016 at 06:56 UTC
Can you please give us an idea of what data is in the files, and an example of what you would like your output to look like? Cheers, R. Pereant, qui ante nos nostra dixerunt!	[reply] [d/l]
Re^2: create a binary matrix by Anonymous Monk on Oct 01, 2016 at 07:14 UTC
there are set of reads in the files but that has nothing to do with the output because with those I have created p.txt. The output I want is like: gene NC_002755.fq NC_009525.fq NC_009565.fq NC_012943.fq N +C_016768.fq NC_016934.fq NC_017026.fq NC_017522.fq NC_017 +523.fq NC_017524.fq NC_017528.fq NC_018078.fq NC_018143.f +q NC_020089.fq NC_020559.fq NC_021054.fq NC_021192.fq +NC_021193.fq NC_021194.fq NC_021251.fq NC_021740.fq NC_02 +2350.fq (3R)-hydroxyacyl-ACP dehydratase subunit HadA 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0 1 0 +0 0 0 0 (3R)-hydroxyacyl-ACP dehydratase subunit HadB 0 0 0 0 0 + 0 1 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 (dimethylallyl)adenosine tRNA methylthiotransferase 1 1 1 +0 0 1 0 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 [download] the result should print 1 if the filename matches else print 0	[reply] [d/l]


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