i have a set of *.lst files. now i want to change the names from "lst" to "dat". how to do it?
ex.:
-rw-r--r-- 1 rram group 22 Sep 21 13:10 a.lst
-rw-r--r-- 1 rram group 22 Sep 21 13:09 b.lst
-rw-r--r-- 1 rram group 22 Sep 21 13:10 c.lst... (4 Replies)
Hi All,
Today I got a small problem while handling zipped files in PROD support.
There are files in this format and I had to grep them reading some contents
A.B.gz.C.D
where A,B,C and D stand for variables (like FIRST.NAME.gz.MIDDLE.LAST).
I know that these files are zipped files and If I... (1 Reply)
directory name = /usr/tom/1997
files -
ABC_1997_ST1_BCD.SQL
BCD_1997_ST1_EFG_SAB.SQL
TTT_EBC_1997_ST1_A.SQL
sub directory - /usr/tom/1997/jan
a) I want to just rename the all files ending with '.SQL' and also its contents in the 1997 directory(excluding subdirectories eg... (3 Replies)
Hello!
I am not familiar with UNIX and I have this problem:
I need to move files from a UNIX machine to a PC. UNIX file names contain ":" as special character which is not recognized in a PC.
How can I change ":" for "_" in the name of a bunch of files in UNIX?
Thanks for your help. (7 Replies)
I have a list of files named ab_*.csv
I would like to remane them all by removing the ab_ and have *.csv
I did the following but I am surely missing something.
/* wrong script */
for i in `ls -1 ab_*`; do mv ab_$i $i; done
Thanks in advance. (1 Reply)
Hi all,
using a utility image file was named starting with blank space and a blank space in between. I want to rename the files.
file names are in the format " sb 12.tif"," sb 13.tif"," sb 14.tif" the files are in thousands. i want to rename as 12.tif, 13.tif, 14.tif....
thanks. (3 Replies)
Hi All
I have a folder that contains hundreds of file with a names
3.msa
4.msa
21.msa
6.msa
345.msa
456.msa
98.msa
...
...
...
I need rename each of this file by adding "core_" in the begiining of each file such as
core_3.msa
core_4.msa
core_21.msa (4 Replies)
Hi,
I have a list of files in a folder with the same name ending (over 1000 files)
joe.jpy.jpeg
joe1.jpy.jpeg
joe2.jpy.jpeg
jon3.jpy.jpeg
jor5.jpy.jpeg
.....jpy.jpeg
etc.
I want to change jpy to hhk
So the output will be:
joe.hhk.jpeg
joe1.hhk.jpeg
joe2.hhk.jpeg
jon3.hhk.jpeg... (3 Replies)
Hello,
I am looking for a command line that will rename name files :
f700_abc_o_t_MASTERID_AS_AE_20130323.csv
like this
f700_abc_o_t_MASTERID_AS_AE_20130324.csv
The great idea could be to get the date stamp 20130323
and change any part of it, instead of just change the... (4 Replies)
Hi,
In sftp script to get files, I have to rename all the files which I am picking. Rename command does not work here. Is there any way to do this?
I am using #!/bin/ksh
For eg: sftp user@host <<EOF
cd /path
get *.txt
rename *.txt *.txt.done
... (7 Replies)
Discussion started by: jhilmil
7 Replies
LEARN ABOUT DEBIAN
bio::searchdist
Bio::SearchDist(3pm) User Contributed Perl Documentation Bio::SearchDist(3pm)NAME
Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object
SYNOPSIS
$dis = Bio::SearchDist->new();
foreach $score ( @scores ) {
$dis->add_score($score);
}
if( $dis->fit_evd() ) {
foreach $score ( @scores ) {
$evalue = $dis->evalue($score);
print "Score $score had an evalue of $evalue
";
}
} else {
warn("Could not fit histogram to an EVD!");
}
DESCRIPTION
The Bio::SearchDist object is a wrapper around Sean Eddy's excellent histogram object. The histogram object can bascially take in a number
of scores which are sensibly distributed somewhere around 0 that come from a supposed Extreme Value Distribution. Having add all the scores
from a database search via the add_score method you can then fit a extreme value distribution using fit_evd(). Once fitted you can then get
out the evalue for each score (or a new score) using evalue($score).
The fitting procedure is better described in Sean Eddy's own code (available from http://hmmer.janelia.org/, or in the histogram.h header
file in Compile/SW). Bascially it fits a EVD via a maximum likelhood method with pruning of the top end of the distribution so that real
positives are discarded in the fitting procedure. This comes from an orginally idea of Richard Mott's and the likelhood fitting is from a
book by Lawless [should ref here].
The object relies on the fact that the scores are sensibly distributed around about 0 and that integer bins are sensible for the histogram.
Scores based on bits are often ideal for this (bits based scoring mechanisms is what this histogram object was originally designed for).
CONTACT
The original code this was based on comes from the histogram module as part of the HMMer2 package. Look at http://hmmer.janelia.org/
Its use in Bioperl is via the Compiled XS extension which is cared for by Ewan Birney (birney@ebi.ac.uk). Please contact Ewan first about
the use of this module
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
add_score
Title : add_score
Usage : $dis->add_score(300);
Function: Adds a single score to the distribution
Returns : nothing
Args :
fit_evd
Title : fit_evd
Usage : $dis->fit_evd();
Function: fits an evd to the current distribution
Returns : 1 if it fits successfully, 0 if not
Args :
fit_Gaussian
Title : fit_Gaussian
Usage :
Function:
Example :
Returns :
Args :
evalue
Title : evalue
Usage : $eval = $dis->evalue($score)
Function: Returns the evalue of this score
Returns : float
Args :
_engine
Title : _engine
Usage : $obj->_engine($newval)
Function: underlyine bp_sw:: histogram engine
Returns : value of _engine
Args : newvalue (optional)
perl v5.14.2 2012-03-02 Bio::SearchDist(3pm)