How would I delete white spaces in a specified file?
Also, I'd like to know what command I would use to take something off a regular expression, and put it onto another.
ie.
.
.
.
expression1 <take_off>
.
.
.
expression2 (put here)
.
.
.
Any help would be great, thanks! (10 Replies)
hi all...
i have the next question:
i have a flat file with a lot of records (lines). Each record has 10 fields, which are separated by pipe (|). My problem is what sometimes, in the first record, there are white spaces (no values, nothing) in the beginning of the record, like this:
ws ws... (2 Replies)
Hi my lovely friends,
Im writing one pgm in which i trying to assign some values like
$var='Jun 6'
but if i do echo of this $var will trim the spaces expect one space.
$echo $var
$Jun 6
But if var='Jun 28', then this will works fine
$echo $var
$Jun 28
this is required to exctract... (2 Replies)
Hi,
Can anybody suggest me how to combine two strings with two or more white spaces and assign it to a variable?
E.g.
first=HAI
second=HELLO
third="$first $second" # appending strings with more than one white spaces
echo $third
this would print
HAI HELLO
Output appears... (2 Replies)
Hi,
How can I remove the unwanted spaces in the line.
123456 789 ABC DEF. - I wanna remove the sapces in this line, I need the output 123456789ABCDEF.
Pls help me...... (3 Replies)
Dear Members,
Following is the code which i am using:
integer i=7
while ((i <= 10 ));
do
param=`echo $TEST_OUT | cut -d"^" -f$i`
a=`echo ${param}`
echo `echo $a | sed 's/+/ /g'`
(( i = i + 1));
done
From the above code TEST_OUT is a variable which has the following value:
... (1 Reply)
friends,
I have a script in solaris 10 SPARC system which is like this
date '+Time: %m/%d/%y %H:%M:%S'
echo " GDBRR GDLRR GDBWR GDLWR GDRRR GDRWR "
sar -b 10 10 |/usr/xpg4/bin/awk '!/Average/ && !/SunOS/ && !/bread/ {$1="";T=$2;T1=$3;T2=$5;T3=$6;T4=$8;T5=$9}{print(T"\t",... (1 Reply)
I have a file which contains certain records about users. the row length is always fixed to 205 characters.
Now I want to read each record line from the file, substring some portion out of it and put into another file. But I have observed that my script is trimming the extra spaces I have used for... (4 Replies)
Hi guys,
when I take substring of a particular data using this command
var=substr($0,11,10)
it comes with spaces, when I am trying to trim the spaces it is not allowing me to do that.
Can you please help me out on that.
As I have to reverse the output of the variable also.
---------- Post... (0 Replies)
Hi All,
I am using following script to name the file base of some values
#!/bin/sh
sourcefile=$1
awk '
BEGIN{ n = 1; name = "FILEFILE12" n ".txt"; }
{
if (substr($0,1,10) == "FILEFILE12")
{
close (name)
n++
a = substr($0,11,10);
b = substr($0,21,5);
name = b "_Src_" a ".txt"
}... (6 Replies)
Discussion started by: manish8484
6 Replies
LEARN ABOUT DEBIAN
bio::graphics::wiggle::loader
Bio::Graphics::Wiggle::Loader(3pm) User Contributed Perl Documentation Bio::Graphics::Wiggle::Loader(3pm)SYNOPSIS
my $loader = Bio::Graphics::Wiggle::Loader->new('/base/directory/for/wigfiles','wibfilename');
my $fh = IO::File->new('uploaded_file.txt');
$loader->load($fh);
my $gff3_file = $loader->featurefile('gff3',$method,$source);
my $featurefile = $loader->featurefile('featurefile');
USAGE
This module loads Bio::Graphics::Wiggle files from source files that use Jim Kent's "WIG" format:
http://genome.ucsc.edu/google/goldenPath/help/wiggle.html
Several data sets can be grouped together in a single WIG source file. The load() method accepts the path to a WIG source file, and will
create one or more .wib ("wiggle binary") databases of quantitative data in the directory indicated when you created the loader. Call the
featurefile() method to return a text file in either GFF3 or Bio::Graphics::FeatureFile format, suitable for loading into a gbrowse
database.
METHODS
$loader = Bio::Graphics::Wiggle::Loader->new('/base/directory' [,'my_data'])
Create a new loader. The first argument specifies the base directory in which the loaded .wib files will be created. The second
argument specifies the base name for the created .wib files, or "track" if not specified.
$loader->load($fh)
Load the data from a source WIG file opened on a filehandle.
$data = $loader->featurefile($type [,$method,$source])
Return the data corresponding to a GFF3 or Bio::Graphics::FeatureFile. The returned file will have one feature per WIG track, and a
properly formatted "wigfile" attribute that directs Bio::Graphics to the location of the quantitative data.
$type is one of "gff3" or "featurefile". In the case of "gff3", you may specify an optional method and source for use in describing
each feature. In the case of "featurefile", the returned file will contain GBrowse stanzas that describe a reasonable starting format
to display the data.
$loader->allow_sampling(1)
If allow_sampling() is passed a true value, then very large files (more than 5 MB) will undergo a sampling procedure to find their
minimum and maximum values and standard deviation. Otherwise, file will be read in its entirety to generate those statistics.
EXTENSIONS
Several extensions to the WIG format "track" declaration are recognized.
transform=<transform>
Specify a transform to be performed on all numeric data within this track prior to loading into the binary wig file. Currently, the
following three declarations are recognized:
transform=logtransform y' = 0 for y == 0
y' = log(y) for y > 0
y' = -log(-y) for y < 0
transform=logsquared y' = log(y**2) for y != 0
y' = 0 for y == 0
transform=none y' = y (no transform - the default)
trim=<trim>
Specify a trimming function to be performed on the data prior to scaling. Currently, the following trim functions are recognized:
trim=stdev1 trim to plus/minus 1 standard deviation of the mean
trim=stdev2 trim to plus/minus 2 standard deviations of the mean (default)
trim=stdevN trim to plus/minus N standard deviations of the mean
trim=none no trimming
Example entended track declaration:
track type=wiggle_0 name="example" description="20 degrees, 2 hr"
trim=stdev2 transform=logsquared
SEE ALSO
Bio::Graphics::Wiggle, Bio::Graphics::Glyph::wiggle_xyplot, Bio::Graphics::Glyph::wiggle_density, Bio::Graphics::Panel,
Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2007 Cold Spring Harbor Laboratory
This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either
version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition,
please see DISCLAIMER.txt for disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Wiggle::Loader(3pm)