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Full Discussion: Separating list of input files (*.file) with a comma in bash script
Top Forums Shell Programming and Scripting Separating list of input files (*.file) with a comma in bash script Post 302526394 by TuAd on Tuesday 31st of May 2011 11:22:34 AM
Old 05-31-2011
Question Separating list of input files (*.file) with a comma in bash script
Hi all,

I'm trying to get a bash script working for a program (bowtie) which takes a list of input files (*.fastq) and assembles them to an output file (outfile.sam). All the .fastq files are in one folder in my home directory (~/infiles).

The problem is that the 'bowtie' requires that the input files are separated by a comma and with no space in between. E.g.:

infile1.fastq,infile2.fastq,infile3.fastq ...


Does anyone know how I could do this?


#!/bin/bash
fn=*.fastq
./bowtie [parameters] index_file ~/infiles/$fn outfile.sam &

How it should run at the end:

./bowtie [parameters] index_file ~/infiles/infile1.fastq,infile2.fastq,infile3.fastq,infile4.fastq outfile.sam


Your help is greatly appreciated!
Best
 

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LEARN ABOUT DEBIAN

bio::tools::run::bowtie::config

Bio::Tools::Run::Bowtie::Config(3pm)			User Contributed Perl Documentation		      Bio::Tools::Run::Bowtie::Config(3pm)

NAME

       Bio::Tools::Run::Bowtie::Config - Configuration data for bowtie commands

SYNOPSIS

       Used internally by Bio::Tools::Run::Bowtie.

DESCRIPTION

       This package exports information describing bowtie commands, parameters, switches, and input and output filetypes for individual bowtie
       commands.

FEEDBACK

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       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Dan Kortschak
       Email dan.kortschak adelaide.edu.au

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

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

perl v5.12.3							    2011-06-18				      Bio::Tools::Run::Bowtie::Config(3pm)
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