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)
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:
and obviously the desired outputs:
Thanks in advance!
1. If I have a file-yyyymmdd.dat in a directory DATA1, then how do I move this file to directory DATA2 and the file name change to file-yyyymmdd.dat.currenttime
I can manual do this
$mv fileA-yyyymmdd.dat ./DATA2/fileA-yyyymmdd.dat.`date +%Y%m%d%H%M%S`
but how do I move all of the files in... (1 Reply)
Using a bash script, I need to find all files in a folder "except" the newest file. Then I need to insert the contents of one text file into all the files found. This text needs to be placed at the beginning of each file and needs a blank line between it and the current contents of the file. Then I... (5 Replies)
I am connecting to a remote server (Unix) and doing a ftp dowmload of files. The script (VB script) works fine except for not being able to move the downloaded files on the remote server to another folder.
I need to move all files with an .asc extesnion from folder "tovecellio_edi" to folder... (1 Reply)
Variations of multiple renames seems to come up a lot but i can't find the answer to this situation.
Tidying up a directory where people rename files to .working, .bob, .attempt1 & so on.
what i am trying to do is: list the file type, & rename from ".whatever" to .fixed.
As the ".whatever" is... (5 Replies)
Hello,
I'm new in the forum and in UNIX scripting, what I need is to write a simple batch script that renames or move the files back & forth from one directory to another, and then schedule the script to run on the server when the scheduled down time is, which is on Thursdays at 8pm and during... (5 Replies)
Hi,
I need to do something easy but I can't seem to figure out how to do this.
Let's say I have 6 files in the directory below:
/ebsbeta_f/flash/EBSUATQB/onlinelog
o1_mf_6_55klt7nr_.log
o1_mf_3_55klskj4_.log
o1_mf_4_55klsrl1_.log
o1_mf_5_55klt09p_.log
o1_mf_2_55klv1ts_.log... (10 Replies)
I have a directory e2e_ms_xfer/cent01
this contains the multiple files some of which will be named below with unique date time stamps
e2e_ms_edd_nom_CCYYMMDD_HHMM.csv
What I want to do is in a loop
1) Get the oldest file
2) Rename
3) Move it up one level from e2e_ms_xfer/cent01 to... (1 Reply)
Hi all,
I have a many folders with zipped files in them. The zipped files are txt files from different folders. The txt files have the same names. If i try to
find . -type f -name "*.zip" -exec cp -R {} /myhome/ZIP \; it fails since the ZIP files from different folders have the same names and... (2 Replies)
I'm using cygwin32 on Windows.
DN is an environment variable pointed at my download directory.
This command works to move the single most recent file in my download directory to my current directory:
mv "`perl -e '$p = $ARGV; opendir $h, $p or die "cannot opendir $p: $!"; @f = sort { -M $a... (2 Replies)
I want to rename (move) multiple files on remote server. I tried the following command to move all TXT files from my_dir directory to /new_dir. But it does not work. Any help?
#!/bin/ksh
sftp -dev3 << ABC
cd my_dir
$(for i in TXT; do echo "ls *.$i" ; rename $x /new_dir/$x;... (1 Reply)
Discussion started by: Soham
1 Replies
LEARN ABOUT DEBIAN
test::regression
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)