AVERAGE_GENOME_SIZE(1) User Commands AVERAGE_GENOME_SIZE(1)NAME
average_genome_size - Calculate the average genome size in Grinder libraries
DESCRIPTION
Usage:
average_genome_size <db_fasta> <rank_file> average_genome_size --help average_genome_size --version
Required arguments:
<db_fasta>
FASTA file containing the full-genomes used to produce the Grinder library.
<rank_file>
Grinder rank file that describes the library composition.
SEE ALSO grinder(7), grinder(1), average_genome_size(1) and change_paired_read_orientation(1).
average_genome_size 0.4.2 May 2012 AVERAGE_GENOME_SIZE(1)
Check Out this Related Man Page
BP_PROCESS_GADFLY(1p) User Contributed Perl Documentation BP_PROCESS_GADFLY(1p)NAME
process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
SYNOPSIS
% process_gadfly.pl ./RELEASE2 > gadfly.gff
DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the
"correct" version of the GFF format.
To use this script, download the whole genome FASTA file and save it to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename.) Do the same for the whole genome
GFF annotation file (the saved file will be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If you wish
you can download the ZIP compressed versions of these files.
Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
(Where "fly" is the name of the database. Change it as appropriate. The database must already exist and be writable by you!)
The resulting database will have the following feature types (represented as "method:source"):
Component:arm A chromosome arm
Component:scaffold A chromosome scaffold (accession #)
Component:gap A gap in the assembly
clone:clonelocator A BAC clone
gene:gadfly A gene accession number
transcript:gadfly A transcript accession number
translation:gadfly A translation
codon:gadfly Significance unknown
exon:gadfly An exon
symbol:gadfly A classical gene symbol
similarity:blastn A BLASTN hit
similarity:blastx A BLASTX hit
similarity:sim4 EST->genome using SIM4
similarity:groupest EST->genome using GROUPEST
similarity:repeatmasker A repeat
IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases.
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_PROCESS_GADFLY(1p)
I have a huge matrix file containing some 1.5 million rows and 6000 columns. The matrix looks something like this:
1 2 3
4 5 6
7 8 9
3 4 5
I want to add all the numbers in the columns of this matrix and display the result to my stdout. This means that the numbers in the first column are:
... (2 Replies)
Hi,
Just trying to get to grips with sed and awk for some reporting for work and I need some assistance:
I have a file that lists policy names on the first line and then on the second line whether the policy is active or not.
Policy Name: Policy1
Active: yes
Policy... (8 Replies)
version info :
vi availabe with RHEL 5.4
I have a text file with 10,000 lines. I want to copy lines from 5000th line to 7000th and redirect to a file. Any idea how I can do this?
Note:
The above scenario is just an example. In my actual requirement, the file has 14 million lines and I want... (9 Replies)
Hi everyone,
I know the following questions are noobish questions but I am asking them because I am confused about the basics of history behind UNIX and LINUX.
Ok onto business, my questions are-:
Was/Is UNIX ever an open source operating system ?
If UNIX was... (21 Replies)
Hello,
I couldn't find an actual introduction thread, so I decided to just put this here.
I go by d0wngrade online. I have been programming in multiple languages for about 15+ years. I started with standard web design languages like HTML and CSS, but I then advanced from design to development... (2 Replies)
Hi guys...
The first active code line in AudioScope.sh is set -u .
This causes a complete exit if a variable is used/found but has not been allocated at the start of the program.
However, apart from writing code to do the task, is there a switch to to check which variables have been... (17 Replies)
Hi.
In thread https://www.unix.com/shell-programming-and-scripting/267833-grouping-counting.html rovf and I had a mini-discussion on grep and awk.
Here is a demo script that compares the awk and grep approaches for this single problem:
#!/usr/bin/env bash
# @(#) s2 Demonstrate group... (1 Reply)
Hello,
I have to fish out some specific columns from a file based on the header value. I have the list of columns I need in a different file. I thought I could read in the list of headers I need,
# file with header names of required columns in required order
headers_file=$2
# read contents... (11 Replies)
For those interested in installing dash shell on OSX Lion to help test POSIX compliancy of shell scripts, it is quite easy. I did it like this:
If you don't have gcc on your system:
0. Download and install the Command Line Tools for Xcode package from Sign In - Apple *
1. Download the dash... (2 Replies)
Hello and thanks in advance for any help anyone can offer me
I'm trying to learn the find command and thought I was understanding it... Apparently I was wrong. I was doing compound searches and I started getting weird results with the -size test. I was trying to do a search on a 1G file owned by... (14 Replies)
I have data of an excel files as given below,
file1
org1_1 1 1 2.5 100
org1_2 1 2 5.5 98
org1_3 1 3 7.2 88
file2
org2_1 1 1 2.5 100
org2_2 1 2 5.5 56
org2_3 1 3 7.2 70
I have multiple excel files as above shown.
I have to copy column 1, column 4 and paste into a new excel file as... (26 Replies)
Dear All,
Taking a break from Vue.js coding for the site, SEO and YT videos; and hopefully addressing some well deserved criticism from some here that I have been too focused on the visual aspects of the forums versus the substance and the community....
While the "current generation... (9 Replies)
Hi all...
Well guys and gals, I jumped in at the deep end and found things that PERL cannot do by default.
Many tricky terminal escape codes are not catered for so I had to create workarounds.
One thing I searched for was this:
Passing perl variable to shell command
AND, @Neo this was... (15 Replies)