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
tree::simple::visitor::pathtoroot
Tree::Simple::Visitor::PathToRoot(3pm) User Contributed Perl Documentation Tree::Simple::Visitor::PathToRoot(3pm)NAME
Tree::Simple::Visitor::PathToRoot - A Visitor for finding the path back a Tree::Simple object's root
SYNOPSIS
use Tree::Simple::Visitor::PathToRoot;
# create an instance of our visitor
my $visitor = Tree::Simple::Visitor::PathToRoot->new();
# pass the visitor to a Tree::Simple object
$tree->accept($visitor);
# now get the accumulated path as a string
# with the '/' character as the delimiter
print $visitor->getPathAsString("/");
# include the tree's trunk in your
# output as well
$visitor->includeTrunk();
# for more complex node objects, you can specify
# a node filter which will be used to extract the
# information desired from each node
$visitor->setNodeFilter(sub {
my ($t) = @_;
return $t->getNodeValue()->description();
});
# you can also get the path back as an array
my @path = $visitor->getPath();
DESCRIPTION
Given a Tree::Simple object, this Visitor will find the path back to the tree's root node.
METHODS
new There are no arguments to the constructor the object will be in its default state. You can use the "includeTrunk" and "setNodeFilter"
methods to customize its behavior.
includeTrunk ($boolean)
Based upon the value of $boolean, this will tell the visitor to collect the trunk of the tree as well.
setNodeFilter ($filter_function)
This method accepts a CODE reference as its $filter_function argument and throws an exception if it is not a code reference. This code
reference is used to filter the tree nodes as they are collected. This can be used to customize output, or to gather specific
information from a more complex tree node. The filter function should accept a single argument, which is the current Tree::Simple
object.
visit ($tree)
This is the method that is used by Tree::Simple's "accept" method. It can also be used on its own, it requires the $tree argument to be
a Tree::Simple object (or derived from a Tree::Simple object), and will throw and exception otherwise.
getPath
This will return the collected path as an array, or in scalar context, as an array reference.
getPathAsString ($delimiter)
This will return the collected path as a string with the path elements joined by a $delimiter. If no $delimiter is specified, the
default (', ') will be used.
BUGS
None that I am aware of. Of course, if you find a bug, let me know, and I will be sure to fix it.
CODE COVERAGE
See the CODE COVERAGE section in Tree::Simple::VisitorFactory for more inforamtion.
SEE ALSO
These Visitor classes are all subclasses of Tree::Simple::Visitor, which can be found in the Tree::Simple module, you should refer to that
module for more information.
AUTHOR
stevan little, <stevan@iinteractive.com>
COPYRIGHT AND LICENSE
Copyright 2004, 2005 by Infinity Interactive, Inc.
<http://www.iinteractive.com>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.10.1 2005-07-14 Tree::Simple::Visitor::PathToRoot(3pm)