Hi,

I have thousands of files in a directory that have the following 2 formats:

289620178.aln
289620179.aln
289620180.aln
289620183.aln
289620184.aln
289620185.aln
289620186.aln
289620187.aln
289620188.aln
289620189.aln
289620190.aln
289620192.aln....

and:

alnCDS_1.fasta
alnCDS_2.fasta
alnCDS_3.fasta
alnCDS_4.fasta
alnCDS_5.fasta
alnCDS_6.fasta
alnCDS_7.fasta
alnCDS_8.fasta
alnCDS_9.fasta
alnCDS_10.fasta....



I am using the following foreach statement to run a perl script like so:

foreach file1 ( *.aln ) ; foreach file2 ( *.fasta )
foreach? ./perl.script.pl $file1 $file2 > $file1$file2.out
foreach? end

This gives me output files

289620178.alnalnCDS_1.fasta.out
289620178.alnalnCDS_2.fasta.out
289620178.alnalnCDS_3.fasta.out .....

when what I want is the following:

289620178.alnalnCDS_1.fasta.out
289620179.alnalnCDS_2.fasta.out
289620180.alnalnCDS_3.fasta.out.... etc...

so that each of the files (*.aln and *.fasta) are sequentially paired as input into the perl script without all of the possible pairs being run through.

Is there a way to do this ?

Thanks!!

That's because your two foreach loops are nested. So each file grabbed from the outer loop is paired with every file in the inner loop and then the next outer loop file gets grabbed and that paired with each file in the inner loop, etc.

The general solution to your problem would be to:

1. First load all the inner loop filenames into an array.

2. Now set up [what was] your outer loop.

3. For each file in your loop (now there's only one loop), take its name, and couple it with the next element in the array using either a counter, or pop, or what ever your script language allows.

quine@sonic.net