01-13-2010
Moving files out of multiple directories and renaming them in numerical order
Hi,
I have 500 directories each with multiple data files inside them. The names are sort of random. For example, one directory has files named e_1.dat, e_5.dat, e_8.dat, etc. I need to move the files to a single directory and rename them all in numerical order, from 1.dat to 1000(or some number).dat. Does anyone know how this could be done? I'm most comfortable with Perl, but any other way of doing it would be perfectly fine.
Thanks!
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hi, I'm trying to write a ksh script to copy a specified number of files from one directory to another.
The files are named in the convention <switchname>_log.<num> and the numbers are sequential single digit onwards. I figured I could find some parameter for ls which would list the files in... (3 Replies)
Discussion started by: Steve_H
3 Replies
2. Shell Programming and Scripting
Hi -
I am new to unix scripts...I need to move several directories on multiple servers to new directories. (0 Replies)
Discussion started by: mackdaddy07
0 Replies
3. Shell Programming and Scripting
Greetings,
I know i can use the mv command to move and rename one file. How can I do this with multiple files?
example
pic01.bmp to pic0001.bmp
how can i perform this function on an entire directory of sequential files and keep them in sequence?
Hints, suggestions are most welcome:)
... (1 Reply)
Discussion started by: rocinante
1 Replies
4. Shell Programming and Scripting
Hi All,
Being new to scripting I am facing a new situation. We have an application that generates a file lets say dumpfile for each user under the users home directory when they execute the application. This is quite a huge file and imagine having that for over 40 users on a daily basis. The... (1 Reply)
Discussion started by: daemongk
1 Replies
5. UNIX for Dummies Questions & Answers
So I am not sure if this should go in the shell forum or in the beginners. It is my first time posting on these forums.
I have a directory, main_dir lets say, with multiple sub directories (one_dir through onehundred_dir for example) and in each sub directory there is a test.txt. How would one... (2 Replies)
Discussion started by: robotsbite
2 Replies
6. UNIX for Dummies Questions & Answers
Hi
I am newbie to unix scripting, but i have enough knowledge to understand.
I have a specific questions like, I use to collect like 3500 files per experiment, each one named like
data_001.img..
data_002.img
data_003.img
....
data_3500.img
I would like to move every 12 files in the 3500... (3 Replies)
Discussion started by: wpat
3 Replies
7. UNIX for Dummies Questions & Answers
Hi, I have a series of files (upwards of 500) the filename format is as follows
CC10-1234P1999.WGS84.p190, all in one directory.
Now the last three numeric characters, in this case 999, can be anything from 001 to 999.
I need to move some of them to a seperate directory, the ones I need to... (5 Replies)
Discussion started by: roche.j.mike
5 Replies
8. Shell Programming and Scripting
Hi experts,
I have a list of files containing forces as the only number as follows.
Force1.txt Force2.txt Force3.txt Force4.txt Force5.txt . . . . . . . . . Force100.txt I want to put all the data(only a number ) in these forces files in the file with the same order like 1,2,3 ..100 .... (2 Replies)
Discussion started by: hamnsan
2 Replies
9. Shell Programming and Scripting
Hi.
I am trying to automate the movement and renaming of a number of files in a directory. I am using the 'mv' command as I do not have access to 'rename'. I have the following scripted FILES=$(ls /transfer/move/sys/mail/20130123/)
if ; then
for i in ${FILES} ; do
mv... (4 Replies)
Discussion started by: jimbojames
4 Replies
10. Shell Programming and Scripting
Hi
I have the following file structure and I want to rename all the abc.jar files to abc_backup.jar
rock@server:~/rakesh> ls -R
.:
test1 test2 test3
./test1:
abc.jar
./test2:
abc.jar
./test3:
abc.jar (2 Replies)
Discussion started by: rakeshkumar
2 Replies
LEARN ABOUT DEBIAN
mclblastline
mclblastline(1) USER COMMANDS mclblastline(1)
NAME
mclblastline - a pipeline for clustering from BLAST files.
SYNOPSIS
mclblastline file-name
mclblastline [deblast options] [pipeline options] file-name
NOTE
mcl has acquired the ability to proceed from label input as produced by mcxdeblast. This enables a very lightweight mechanism of generating
clusterings from BLAST files. You might want to use this mechanism, documented in the mcl manual.
NOTE
mclblastline used to require (given default parameters) the presence of the zoem macro processor to produce detailed output. This is no
longer the case. By default mclblastline now creates a line-based tab-separated dump file. Zoem will be invoked when the --fmt-fancy option
is supplied. In that case, zoem obviously has to be installed.
DESCRIPTION
mclblastline wraps around mclpipeline. It supplies the --parser=app and --parser-tag=str options, setting them respectively to mcxdeblast
and blast. This tells mclpipeline to use mcxdeblast as the parse script in its pipeline. The significance of the blast tag is that any
mcxdeblast option can be passed through mclblastline and mclpipeline by inserting this tag into the option. For example, mcxdeblast accepts
the --score=x option. When using mclblastline, you specify it as --blast-score=x. There are two exceptions to this rule, namely the --xi-
dat=str and --xo-dat=str options. Refer to the mclpipeline manual for more information.
Additionally, all mclpipeline options are acceptable to mcxdeblast as well. The --whatif is useful for getting a feel for the pipeline. The
--mcl-I=f inflation option and --mcl-scheme=i scheme index options are your basic means for respectively manipulating cluster granularity
and allocating resources. Read the mcl manual entries for a description of the corresponding -I and -scheme mcl options.
The best advice is to glance over the mcxdeblast and mclpipeline options in order to get a feeling for which of those may come in handy for
you. Then start experimenting. Use the --whatif option, it will tell you what would happen without actually doing it.
OPTIONS
All mcxdeblast and mclpipeline options. mcxdeblast options must be passed using the mechanism described above.
EXAMPLES
mclblastline --blast-score=b
--blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile
This will use bit scores, sort cluster indices such that the corresponding labels are ordered alphabetically, ignore bit scores not exceed-
ing 5, and use inflation value 2.5. In this case, the output clustering will be in the file named myblastfile.I25s2 (I25 identifying the
inflation value and s2 identifying the resource scheme) and the formatted output will be in the file myblastfile.I25s2.fmt.
mclblastline --prepare-mcl myblastfile
mclblastline --start-mcl --mcl-I=1.2 myblastfile
mclblastline --start-mcl --mcl-I=1.6 myblastfile
mclblastline --start-mcl --mcl-I=2.0 myblastfile
mclblastline --start-mcl --mcl-I=2.4 myblastfile
mclblastline --start-mcl --mcl-I=2.8 myblastfile
etc ..
The first run prepares an input matrix to be read by mcl. In this case its file will be named myblastfile.sym. The subsequent runs use
this matrix. CAVEAT there are some options that you need to repeat when executing such a resumed run. They are clearly marked in the
mclpipeline manual - namely those options that affect names of (intermediate) files. Most importantly, this concerns the mclpipeline options
that have prefix --xo or --xi. For example,
mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=1.2 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=1.6 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.0 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.4 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.8 myblastfile
etc ..
In this case, the matrix file will be named myblastfile.b.sym, and the --xo-dat options must be repeated in all runs so that the pipeline
reconstructs the correct file name(s).
AUTHOR
Stijn van Dongen
SEE ALSO
mcxdeblast, mclpipeline, mcxassemble.
mclblastline 12-068 8 Mar 2012 mclblastline(1)