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
cmdtest
CMDTEST(1) General Commands Manual CMDTEST(1)NAME
cmdtest - blackbox testing of Unix command line tools
SYNOPSIS
cmdtest [-c=COMMAND] [--command=COMMAND] [--config=FILE] [--dump-config] [--dump-memory-profile=METHOD] [--dump-setting-names]
[--generate-manpage=TEMPLATE] [-h] [--help] [-k] [--keep] [--list-config-files] [--log=FILE] [--log-keep=N] [--log-level=LEVEL]
[--log-max=SIZE] [--no-default-configs] [--output=FILE] [-t=TEST] [--test=TEST] [--timings] [--version] [FILE]...
DESCRIPTION
cmdtest black box tests Unix command line tools. Given some test scripts, their inputs, and expected outputs, it verifies that the command
line produces the expected output. If not, it reports problems, and shows the differences.
Each test case foo consists of the following files:
foo.script
a script to run the test (this is required)
foo.stdin
the file fed to standard input
foo.stdout
the expected output to the standard output
foo.stderr
the expected output to the standard error
foo.exit
the expected exit code
foo.setup
a shell script to run before the test
foo.teardown
a shell script to run after test
Usually, a single test is not enough. All tests are put into the same directory, and they may share some setup and teardown code:
setup-once
a shell script to run once, before any tests
setup a shell script to run before each test
teardown
a shell script to run after each test
teardown-once
a shell script to run once, after all tests
cmdtest is given the name of the directory with all the tests, or several such directories, and it does the following:
o execute setup-once
o for each test case (unique prefix foo):
-- execute setup
-- execute foo.setup
-- execute the command, by running foo.script, and redirecting standard input to come from foo.stdin, and capturing standard output
and error and exit codes
-- execute foo.teardown
-- execute teardown
-- report result of test: does exit code match foo.exit, standard output match foo.stdout, and standard error match foo.stderr?
o execute teardown-once
Except for foo.script, all of these files are optional. If a setup or teardown script is missing, it is simply not executed. If one of
the standard input, output, or error files is missing, it is treated as if it were empty. If the exit code file is missing, it is treated
as if it specified an exit code of zero.
The shell scripts may use the following environment variables:
DATADIR
a temporary directory where files may be created by the test
TESTNAME
name of the current test (will be empty for setup-once and teardown-once)
SRCDIR directory from which cmdtest was launched
OPTIONS -c, --command=COMMAND
ignored for backwards compatibility
--config=FILE
add FILE to config files
--dump-config
write out the entire current configuration
--dump-memory-profile=METHOD
make memory profiling dumps using METHOD, which is one of: none, simple, meliae, or heapy (default: simple)
--dump-setting-names
write out all names of settings and quit
--generate-manpage=TEMPLATE
fill in manual page TEMPLATE
-h, --help
show this help message and exit
-k, --keep
keep temporary data on failure
--list-config-files
list all possible config files
--log=FILE
write log entries to FILE (default is to not write log files at all); use "syslog" to log to system log
--log-keep=N
keep last N logs (10)
--log-level=LEVEL
log at LEVEL, one of debug, info, warning, error, critical, fatal (default: debug)
--log-max=SIZE
rotate logs larger than SIZE, zero for never (default: 0)
--no-default-configs
clear list of configuration files to read
--output=FILE
write output to FILE, instead of standard output
-t, --test=TEST
run only TEST (can be given many times)
--timings
report how long each test takes
--version
show program's version number and exit
EXAMPLE
To test that the echo(1) command outputs the expected string, create a file called echo-tests/hello.script containing the following con-
tent:
#!/bin/sh
echo hello, world
Also create the file echo-tests/hello.stdout containing:
hello, world
Then you can run the tests:
$ cmdtest echo-tests
test 1/1
1/1 tests OK, 0 failures
If you change the stdout file to be something else, cmdtest will report the differences:
$ cmdtest echo-tests
FAIL: hello: stdout diff:
--- echo-tests/hello.stdout 2011-09-11 19:14:47 +0100
+++ echo-tests/hello.stdout-actual 2011-09-11 19:14:49 +0100
@@ -1 +1 @@
-something else
+hello, world
test 1/1
0/1 tests OK, 1 failures
Furthermore, the echo-tests directory will contain the actual output files, and diffs from the expected files. If one of the actual output
files is actually correct, you can actualy rename it to be the expected file. Actually, that's a very convenient way of creating the ex-
pected output files: you run the test, fixing things, until you've manually checked the actual output is correct, then you rename the file.
SEE ALSO cliapp(5).
CMDTEST(1)