some help on the following perl script - perl

Question

Need help in merging/concatenating /combining /binding etc
I have several ascii files each defining one variable which I have converted to a single column array
I have such columnised data for many variables ,so I need to perform a column bind like R does and make it one single file.
I can do the same in R but there are too many files. Being able to do it with one single code will help save a lot of time.
Using the following code ,new to perl and need help with this.
#filenames = ("file1.txt","file2.txt");
open F2, ">file_combined.txt" or die;
for($j = 0; $j< scalar #filenames;$j++){
open F1, $filenames[$j] or die;
for($i=1;$i<=6;$i++){$line=<F1>;}
while($line=<F1>){
chomp $line;
#spl = split '\s+', $line;
for($i=0;$i<scalar #spl;$i++){
print F2 "$spl[$i]\n";
paste "file_bio1.txt","file_bio2.txt"> file_combined.txt;
}
}
close F1;
}
Input files here are Ascii text files of a raster.They look like this
32 12 34 21 32 21 22 23
12 21 32 43 21 32 21 12
The above mentioned code without the paste syntax converts these files into a single column
32
12
34
21
32
21
22
23
12
21
32
43
21
32
21
12
The output should look like this
12 21 32
32 23 23
32 21 32
12 34 12
43 32 32
32 23 23
32 34 21
21 32 23
Each column represents a different ascii file.
I need around 15 such ascii files into one dataframe.I can do the same in R but it consumes a lot of time as the number of files and regions of interest are too many and the files are a bit large too.

Answer 1

Let's step through what you have...
# files you want to open for reading..
#filenames = ("file1.txt","file2.txt");
# I would use the 3 arg lexical scoped open
# I think you want to open this for 'append' as well
# open($fh, ">>", "file_combined.txt") or die "cannot open";
open F2, ">file_combined.txt" or die;
# #filenames is best thought as a 'list'
# for my $file (#filenames) {
for($j = 0; $j< scalar #filenames;$j++){
# see above example of 'open'
# - $filenames[$j] + $file
open F1, $filenames[$j] or die;
# what are you trying to do here? You're overriding
# $line in the next 'while loop'
for($i=1;$i<=6;$i++){$line=<F1>;}
# while(<$fh1>) {
while($line=<F1>){
chomp $line;
# #spl is short for split?
# give '#spl' list a meaningful name
#spl = split '\s+', $line;
# again, #spl is a list...
# for my $word (#spl) {
for($i=0;$i<scalar #spl;$i++){
# this whole block is a bit confusing.
# 'F2' is 'file_combined.txt'. Then you try and merge
# ( and overwrite the file) with the paste afterwards...
print F2 "$spl[$i]\n";
# is this a 'system call'?
# Missing 'backticks' or 'system'
paste "file_bio1.txt","file_bio2.txt"> file_combined.txt;
}
}
# close $fh1
close F1;
}
# I'm assuming there's a 'close F2' somewhere here..
It looks like you're trying to do this:
#filenames = ("file1.txt","file2.txt");
$oufile = "combined_text.txt";
`paste $filenames[0] $filenames[1] > $outfile`;