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Full Discussion: Two variables in output file name nested for loops
Top Forums Shell Programming and Scripting Two variables in output file name nested for loops Post 302646011 by aminards on Thursday 24th of May 2012 11:33:23 AM
Old 05-24-2012
Question Two variables in output file name nested for loops
I am trying to use two nested for loops to process some files and then create a new file using both variables in the output file name. I have several files in this naming style:
Code:
S1_L3_all_R1.fastq
S1_L3_all_R2.fastq
S1_L4_all_R1.fastq
S1_L4_all_R2.fastq
.
.
S1_L8_all_R1.fastq
S1_L8_all_R1.fastq

I need to apply a process to each file and rename the files like this:
Code:
S1_L3_all_R1.fasta
S1_L3_all_R2.fasta
.
.
S1_L8_all_R1.fasta
S1_L8_all_R2.fasta

I am using BASH. Here is what I have tried:

Code:
for((n=3;n<=8;n++))
do 
for((k=1;k<=2;k++))
do 
for f  in S1_L$n_all_filt_R*.fastq
do 
echo $f
cat $f | perl -e my file processing > S1_L$n_all_filt_R$k.fasta
done
done
done


This runs through the file processing for each file but the file name is S1_L1.fasta and this file name is recycled for each of my original files. It seems to me that everything after the first variable in my output file name is ignored.

How can I use two variables in a file name to get the output file names I am looking for?
Last edited by Scrutinizer; 05-24-2012 at 04:41 PM.. Reason: Removed times roman formatting
 

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LEARN ABOUT DEBIAN

bio::alignio::fasta

Bio::AlignIO::fasta(3pm)				User Contributed Perl Documentation				  Bio::AlignIO::fasta(3pm)

NAME

       Bio::AlignIO::fasta - fasta MSA Sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

DESCRIPTION

       This object can transform Bio::SimpleAlign objects to and from fasta flat file databases.  This is for the fasta alignment format, not for
       the FastA sequence analysis program.  To process the alignments from FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.

FEEDBACK

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Peter Schattner

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln
	Function: returns the next alignment in the stream.
	Returns : Bio::Align::AlignI object - returns 0 on end of file
		       or on error
	Args	: -width => optional argument to specify the width sequence
		  will be written (60 chars by default)

       See Bio::Align::AlignI

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in fasta format
	Returns : 1 for success and 0 for error
	Args	: L<Bio::Align::AlignI> object

       See Bio::Align::AlignI

   _get_len
	Title	: _get_len
	Usage	:
	Function: determine number of alphabetic chars
	Returns : integer
	Args	: sequence string

   width
	Title	: width
	Usage	: $obj->width($newwidth)
		  $width = $obj->width;
	Function: Get/set width of alignment
	Returns : integer value of width
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.2							    2012-03-02						  Bio::AlignIO::fasta(3pm)
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