All,
I'm a newbie at shell scripting and regular expressions and I just need to take a file that's arranged like the one below, remove all leading and trailing whitespace and add a line break after each word. I've been able to remove a few spaces using various awk, sed and Perl scripts, but... (7 Replies)
Hi,
I have been trying to remove whitespace from a file using sed. Here is an example of what im trying to do:
www1 = www1
www2 = www2
www3 = www3
and all the way to 300 and i want it to look like:
www1=www1
www2-www2
www3=www3
again upto 300
Any help... (12 Replies)
Hmmm... Bash doesn't parse whitespace with a read.
lev@sys09:~$ read line; echo "$line"
test
test
You can imagine what this does if you're using a shell script to read a list of unknown file names containing unknown spaces.
lev@sys09:~$ read word1 word2; echo "$word1,$word2"
123 456... (2 Replies)
Hello forums!
I've been tinkering with a shell script to partition and restore content to a drive based on a type of file in a given directory. My goal is for my script to assemble several restore images, partition the drive based on the images and to then restore those images to the partitions... (1 Reply)
I combined 2 files using the paste command. It gave me something like this:
123445 ,AABBNN
22344 ,BBVVMM
I want to remove the whitespace between the end of string 1 and the comma (there is more blank space than my post is showing). Would I... (2 Replies)
I have a single string as below:
Rat run after Cat
i.e. there is a single whitespace after Cat.
This causes my file to fail.
Is there a way I can remove any whitespace at the end of any string.
I tried sed 's/ *//g', but it removes all white space and the above string becomes... (10 Replies)
Hi
Following is an example line.
echo "192.22.22.22 \"33dffwef\" 200 300 dsdsd" | sed "s:\(\ *\ \):\1:"
I want it's output to be
200
However this is not the case. Can you tell me how to do it? I don't want to use AWK for this. Secondly, how can i fetch just 300? Should I use "\2"... (3 Replies)
Hello I am working aon script, that tells me how many users or on the system when i run it.
The script is
#!/bin/bash
w | cut -f 1 -d ' ' |sort -u | wc -l
When ran it shows 16 users including myself and a line of white space.
I was wondering what I need to add to remove my user... (2 Replies)
Hi guys,
I am working with large data sets and often times realize that not all of the columns are aligned correctly (sometimes rows will be shifted). So when I try to do something like:
awk '{ if ($2 > 30 && $5 == $3){print}}' file > output
it won't really work since some of the rows... (2 Replies)
This is my file
.........hostname.............this is hostname
.........alias...................alias name
Remark use dot(.) instead of whitespace B'cuz this forum not allow to use more whitespace.
---------------------------------------
I sperate by whitespace not work.
awk 'BEGIN {FS=" "}... (4 Replies)
Discussion started by: cyberking
4 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)