Merge the files with the same file name in Perl [closed] - perl

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I currently got a problem on merging the files in Perl.
There are two directories/folders, which contain the same name and extension files in pairs.
For example, in folder 1, I have files 1.fastq, 2.fastq,....,10.fastq.
In folder 2, I have the exactly same file names 1.fastq, 2.fastq,....,10.fastq, but they contain different information.
I want to merge the files with the same name, in the beginning I tried the cat command
$ cat 1.fastq 1.fastq > 1.fastq
However if there are too many files, for example 1000+, I will need to do it 1000+ times.
How can I do it automatically with the perl command?
Thank you in advance.

Answer 1

Perl based solution will be like below.
#!/usr/bin/perl
$source_dir = "./source";
$dest_dir = "./dest";
opendir ($source, $source_dir);
#source_files = readdir $source;
foreach $each_file (#source_files){
if($each !~ /^(\.|\.\.)$/) {
open $file_h , "< $source_dir/$each_file";
#contents = <$file_h>;
open $dest_file, ">>$dest_dir/$each_file";
print $dest_file #contents;
#contents =();
}
}
You can also do this using Shell script also. A typical shell script will be like below.
#!/usr/bin/sh
source='./source'
dest='./dest'
for file in `ls $source`
do
if [ -e $dest/$file ]
then
cat $source/$file $dest/$file >> $dest/$file."unique_name"
rm $dest/$file
mv $dest/$file."unique_name" $dest/$file
else
cp $source/$file $dest/$file
fi
done
You can not use input file as output with cat.
$ cat 1.fastq 1.fastq > 1.fastq
This will lead you error saying "input file is output file".