Sponsored Content
Top Forums UNIX for Dummies Questions & Answers Help with BASH/AWK queries .... Post 302477394 by Fahmida on Saturday 4th of December 2010 11:08:45 PM
Old 12-05-2010
Help with BASH/AWK queries ....

Hi Everyone,

I have an input file in the following format:
score.file1.txt
HTML Code:
contig00045 length=566   numreads=19    1047    0.0
contig00055 length=524   numreads=7    793    0.0
contig00052 length=535   numreads=10    607    e-176
contig00072 length=472   numreads=46    571    e-165
contig00019 length=667   numreads=5    474    e-136
I've a second file:
data.file1.txt
HTML Code:
>contig00045 length=566   numreads=19
GGGCTGACGTGCCGCTAATACGACTCACTATAGGGAGAGCATAAAACACG
CCTCCTGAGCTGCAGCAGAAAAAGAGACTCCCCTTGAGCTTTCAGATTGA
>contig00055 length=524   numreads=7
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGAGGGAGGAT
GCTGGAC
>contig00052 length=535   numreads=10
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGGATGTCCAC
AGGCAGAGGGATGTCCACAGGCAGAGGGATGCCACAGGCA
>contig00072 length=472   numreads=46
TTTAGCTGCTTTCCCCCGGAGGAGATTTGAATTCCGGTGAAATCCAGGCT
TTGTTCATTTTAATAAGCGTCAGCCTGTCAGCGCTGTCAGTTGACAGGCG
>contig00019 length=667   numreads=5
TATAGGGAGAGTGGCATTCTAATAACAGGGGACGGGGGCAGAGGACTCTC
GCTGACCGTCCCATGTAAGGGTGGTGTCGGAT
This file contains a header (>contig00045 length=566 numreads=19) followed by few lines of sequence.

In the first file (score.file1.txt), for each row the fourth column is score1(1047, 793, 607,571 etc.) and 5th column is score2 (0.0, 0.0, e-176, e-165 etc.).
I would like to extract those TWO data (from data.file1.txt) based on TOP score1 and if their score2 is NOT 0.0.

For example based on the above data, my desired output is:
output.file1.txt
HTML Code:
>contig00052 length=535   numreads=10
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGGATGTCCAC
AGGCAGAGGGATGTCCACAGGCAGAGGGATGCCACAGGCA
>contig00072 length=472   numreads=46
TTTAGCTGCTTTCCCCCGGAGGAGATTTGAATTCCGGTGAAATCCAGGCT
TTGTTCATTTTAATAAGCGTCAGCCTGTCAGCGCTGTCAGTTGACAGGCG
Thanks in advance.
 

10 More Discussions You Might Find Interesting

1. UNIX for Advanced & Expert Users

Some queries...

Guys need some advice on how to check some of the questions below? i'm running on an open VMS platform... which i am an idiot to... appreciate if anyone can give some hints or source on how to check on.. a script that is running on cron job... but doesn't run as the login user name.. 1. why... (6 Replies)
Discussion started by: 12yearold
6 Replies

2. UNIX for Advanced & Expert Users

Two small queries

Query 1 : How to check if a directory already exists? If doesn't exist then create a new one. Query 2 : I want to put following text using a single echo statement into a log file and also want to retain the formatting of the text. How it can be... (3 Replies)
Discussion started by: skyineyes
3 Replies

3. Shell Programming and Scripting

my queries

hi guys Well, i need to have a report generation script or any script which will show me all the content/information of a file when i run that script. Please help me on this isssue at the earliest.As i am little bit aware of scripting.Thanks in advance! regards ash (4 Replies)
Discussion started by: whizkidash
4 Replies

4. Homework & Coursework Questions

Queries

Any help on like where to get started on this? I'm just confused. 1. The problem statement, all variables and given/known data: Enter text here.Queries to satisfy these two report requests (use your CCI database): Retrieve all rows of active inventory where current on hands is less than... (0 Replies)
Discussion started by: lakers34kb
0 Replies

5. UNIX for Advanced & Expert Users

awk script queries

Hi, First query: I am trying to execute the below command to pull all the record whose length is not of the expected. But this is not giving the expected results. $2 is the record length passed in the script as second parameter.$filename is the filename on which the awk is executed.It is... (4 Replies)
Discussion started by: devina
4 Replies

6. Shell Programming and Scripting

Few queries regarding awk...

One of the command output is as below. -rw-r--r--+ 1 root root 75G Nov 21 16:43 /var/ovs/mount/86BXXX/running_pool/Machine1/System-sda.img -rw-r--r--+ 1 root root 75G Nov 21 16:36 /var/ovs/mount/86BXXX/running_pool/Machine2/System.img -rw-r--r--+ 1 root root 150G Sep 23 19:13... (2 Replies)
Discussion started by: pinga123
2 Replies

7. UNIX for Advanced & Expert Users

How many DNS queries

Is there any way to see how many queries come into our external DNS server? In looking at DNS providers, most of them base pricing on number of queries per month so I just wanted to see if you had any idea/way of gathering that data? A rough ballpark figure would even work. Our DNS server is... (1 Reply)
Discussion started by: raggmopp
1 Replies

8. UNIX for Dummies Questions & Answers

FTP Queries

Hi, 1) How to get exact permissions, group names for files while transferring with FTP 2) Is there any command to transfer entire directory and sub directories. Thanks (1 Reply)
Discussion started by: nag_sathi
1 Replies

9. Debian

GRUB Queries ?!

Hello, I am posting the following questions here because I need them answered by people who have actually done a lot of work in GRUB. DO NOT GIVE ME GUESS ANSWERS PLEASE. Feel free to redirect me if this is not the right place to ask these questions. Can I download GRUB separately from... (6 Replies)
Discussion started by: sreyan32
6 Replies

10. IP Networking

RDNS Queries

Hey everyone, I have a question, I've been playing around with tcpdump, and noticed my machine making numerous rdns look ups. They are displayed like: 10.80.80.141.51234 > 10.80.80.1.domain: 9950+ PTR? 223.114.55.65.in-addr.arpa. (44) My question is, if dns works based on numerical... (0 Replies)
Discussion started by: Lost in Cyberia
0 Replies
Graphics::Primitive::Component(3pm)			User Contributed Perl Documentation		       Graphics::Primitive::Component(3pm)

NAME
Graphics::Primitive::Component - Base graphical unit DESCRIPTION
A Component is an entity with a graphical representation. SYNOPSIS
my $c = Graphics::Primitive::Component->new({ origin => Geometry::Primitive::Point->new({ x => $x, y => $y }), width => 500, height => 350 }); LIFECYCLE
prepare Most components do the majority of their setup in the prepare. The goal of prepare is to establish it's minimum height and width so that it can be properly positioned by a layout manager. $driver->prepare($comp); layout This is not a method of Component, but a phase introduced by the use of Layout::Manager. If the component is a container then each of it's child components (even the containers) will be positioned according to the minimum height and width determined during prepare. Different layout manager implementations have different rules, so consult the documentation for each for details. After this phase has completed the origin, height and width should be set for all components. $lm->do_layout($comp); finalize This final phase provides and opportunity for the component to do any final changes to it's internals before being passed to a driver for drawing. An example might be a component that draws a fleuron at it's extremities. Since the final height and width isn't known until this phase, it was impossible for it to position these internal components until now. It may even defer creation of this components until now. It is not ok to defer all action to the finalize phase. If you do not establish a minimum hieght and width during prepare then the layout manager may not provide you with enough space to draw. $driver->finalize($comp); draw Handled by Graphics::Primitive::Driver. $driver->draw($comp); METHODS
Constructor new Creates a new Component. Instance Methods background_color Set this component's background color. border Set this component's border, which should be an instance of Border. callback Optional callback that is fired at the beginning of the "finalize" phase. This allows you to add some sort of custom code that can modify the component just before it is rendered. The only argument is the component itself. Note that changing the position or the dimensions of the component will not re-layout the scene. You may have weird results of you manipulate the component's dimensions here. class Set/Get this component's class, which is an abitrary string. Graphics::Primitive has no internal use for this attribute but provides it for outside use. color Set this component's foreground color. fire_callback Method to execute this component's "callback". get_tree Get a tree for this component. Since components are -- by definiton -- leaf nodes, this tree will only have the one member at it's root. has_callback Predicate that tells if this component has a "callback". height Set this component's height. inside_bounding_box Returns a Rectangle that defines the edges of the 'inside' box for this component. This box is relative to the origin of the component. inside_height Get the height available in this container after taking away space for padding, margin and borders. inside_width Get the width available in this container after taking away space for padding, margin and borders. margins Set this component's margins, which should be an instance of Insets. Margins are the space outside the component's bounding box, as in CSS. The margins should be outside the border. maximum_height Set/Get this component's maximum height. Used to inform a layout manager. maximum_width Set/Get this component's maximum width. Used to inform a layout manager. minimum_height Set/Get this component's minimum height. Used to inform a layout manager. minimum_inside_height Get the minimum height available in this container after taking away space for padding, margin and borders. minimum_inside_width Get the minimum width available in this container after taking away space for padding, margin and borders. minimum_width Set/Get this component's minimum width. Used to inform a layout manager. name Set this component's name. This is not required, but may inform consumers of a component. Pay attention to that library's documentation. origin Set/Get the origin point for this component. outside_height Get the height consumed by padding, margin and borders. outside_width Get the width consumed by padding, margin and borders. finalize Method provided to give component one last opportunity to put it's contents into the provided space. Called after prepare. padding Set this component's padding, which should be an instance of Insets. Padding is the space inside the component's bounding box, as in CSS. This padding should be between the border and the component's content. page If true then this component represents stand-alone page. This informs the driver that this component (and any children) are to be renderered on a single surface. This only really makes sense in formats that have pages such as PDF of PostScript. prepare Method to prepare this component for drawing. This is an empty sub and is meant to be overridden by a specific implementation. preferred_height Set/Get this component's preferred height. Used to inform a layout manager. preferred_width Set/Get this component's preferred width. Used to inform a layout manager. to_string Get a string representation of this component in the form of: $name $x,$y ($widthx$height) visible Set/Get this component's visible flag. width Set/Get this component's width. AUTHOR
Cory Watson, "<gphat@cpan.org>" BUGS
Please report any bugs or feature requests to "bug-geometry-primitive at rt.cpan.org", or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Geometry-Primitive <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Geometry-Primitive>. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. COPYRIGHT &; LICENSE Copyright 2008-2009 by Cory G Watson. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.12.3 2011-06-02 Graphics::Primitive::Component(3pm)
All times are GMT -4. The time now is 04:11 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy