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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::seqio::fasta

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

NAME

       Bio::SeqIO::fasta - fasta sequence input/output stream

SYNOPSIS

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

DESCRIPTION

       This object can transform Bio::Seq objects to and from fasta flat file databases.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   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 - Ewan Birney &; Lincoln Stein
       Email: birney@ebi.ac.uk
	      lstein@cshl.org

CONTRIBUTORS

       Jason Stajich, jason-at-bioperl.org

APPENDIX

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

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object, or nothing if no more available
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: Writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Array of 1 or more Bio::PrimarySeqI objects

   width
	Title	: width
	Usage	: $obj->width($newval)
	Function: Get/Set the line width for FASTA output
	Returns : value of width
	Args	: newvalue (optional)

   preferred_id_type
	Title	: preferred_id_type
	Usage	: $obj->preferred_id_type('accession')
	Function: Get/Set the preferred type of identifier to use in the ">ID" position
		  for FASTA output.
	Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
		  Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
	Args	: string when setting. This must be one of values defined in
		  @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
		  accession, accession.version, display, primary
	Throws	: fatal exception if the supplied id type is not in @SEQ_ID_TYPES.

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