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Top Forums Shell Programming and Scripting SBATCH trinity for multiple files and rename/move the output files Post 302980058 by @man on Tuesday 23rd of August 2016 10:39:10 AM
Old 08-23-2016
Code SBATCH trinity for multiple files and rename/move the output files

Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
Code:
#!/bin/bash -l
#SBATCH -p node
#SBATCH -A <projectID>
#SBATCH -n 16
#SBATCH -t 7-00:00:00
#SBATCH --mem=128GB 
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<email address>
#SBATCH -o /path/to/log/file
#SBATCH -e /path/to/error/file
#SBATCH -J trinity

module load bioinfo-tools trinity

Trinity --seqType fq --max_memory 120G --CPU 16 \
--left /path/to/first/input/input1.fq \
--right /path/to/second/input/input2.fq \
--normalize_reads --SS_lib_type RF --no_bowtie --output /path/to/output/directory/trinity_out_dir

Now I cannot figure out how to modify this to take multiple files (2 inputs in each iteration) and then rename the output file (which is "trinity.fasta") and move it to another folder so it won't be overwritten every time.
all my files are like this:
Code:
Sample1_1.fq
Sample1_2.fq

sample2_1.fq
Sample2_2.fq
...

and obviously the desired outputs:
Code:
Sample1.fasta, Sample2.fasta, ...

Thanks in advance!
 

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Test::Regression(3pm)					User Contributed Perl Documentation				     Test::Regression(3pm)

NAME
Test::Regression - Test library that can be run in two modes; one to generate outputs and a second to compare against them VERSION
Version 0.05 SYNOPSIS
use Test::Regression; ok_regression(sub {return "hello world"}, "t/out/hello_world.txt"); DESCRIPTION
Using the various Test:: modules you can compare the output of a function against what you expect. However if the output is complex and changes from version to version, maintenance of the expected output could be costly. This module allows one to use the test code to generate the expected output, so that if the differences with model output are expected, one can easily refresh the model output. EXPORT
ok_regression FUNCTIONS
ok_regression This function requires two arguments: a CODE ref and a file path. The CODE ref is expected to return a SCALAR string which can be compared against previous runs. If the TEST_REGRESSION_GEN is set to a true value, then the CODE ref is run and the output written to the file. Otherwise the output of the file is compared against the contents of the file. There is a third optional argument which is the test name. ENVIRONMENT VARIABLES
TEST_REGRESSION_GEN If the TEST_REGRESSION_GEN environment file is unset or false in a perl sense, then the named output files must exist and be readable and the test will run normally comparing the outputs of the CODE refs against the contents of those files. If the environment variable is true in a perl sense, then model output files will be overwritten with the output of the CODE ref. AUTHOR
Nicholas Bamber, "<nicholas at periapt.co.uk>" BUGS
Please report any bugs or feature requests to "bug-test-regression at rt.cpan.org", or through the web interface at <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Test-Regression>. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. testing of STDERR The testing of stderr from this module is not as thorough as I would like. Test::Builder::Tester allows turning off of stderr checking but not matching by regular expression. Handcrafted efforts currently fall foul of Test::Harness. Still it is I believe adequately tested in terms of coverage. SUPPORT
You can find documentation for this module with the perldoc command. perldoc Test::Regression You can also look for information at: o RT: CPAN's request tracker <http://rt.cpan.org/NoAuth/Bugs.html?Dist=Test-Regression> o AnnoCPAN: Annotated CPAN documentation <http://annocpan.org/dist/Test-Regression> o CPAN Ratings <http://cpanratings.perl.org/d/Test-Regression> o Search CPAN <http://search.cpan.org/dist/Test-Regression/> ACKNOWLEDGEMENTS
Some documentation improvements have been suggested by toolic (http://perlmonks.org/?node_id=622051). Thanks to Filip GraliXski for pointing out I need to test against output of zero length and providing a patch. COPYRIGHT &; LICENSE Copyright 2009-10 Nicholas Bamber. This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License. See http://dev.perl.org/licenses/ for more information. perl v5.10.1 2010-08-29 Test::Regression(3pm)
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