Many of the Perl scripts require that the VCF files are compressed by bgzip and indexed by tabix (both tools are part of the tabix package, available for download here). The VCF files can be compressed and indexed using the following commands

bgzip my_file.vcf
tabix -p vcf my_file.vcf.gz

http://vcftools.sourceforge.net/perl_module.html

Address of the bookmark: http://vcftools.sourceforge.net/perl_module.html

'du' – Check the size of a directory

$ du
This command ( du) gives you a list of directories that exist in the current working directory along with their sizes in kilobytes (default). The last line of the output gives you the total size of the current directory including its subdirectories.

$ du /home/jin1
The above command would give you the directory size of the directory /home/david

$ du -h
The same “du”command with some flag gives you a better output than the default one. The option '-h' stands for human readable format. Therefore, in order to print the sizes of the files / directories in your desire notation use this time suffixed with a 'k' if its kilobytes and 'M' if its Megabytes and 'G' if its Gigabytes.

$ du -ah
If you are interested in checking everything present in a folder use above mentioned command. It gives us not only the directories but also all the files that are present in the current directory. The “-a” flag displays the filenames along with the directory names in the output.

$ du -c
This gives you a grand total as the last line of the output. So if your directory occupies 30MB the last 2 lines of the output would be 30M.

$ du -s
Use this command to displays a summary of the directory size. It is the simplest way to know the total size of the current directory.

$ du -S
This would display the size of the current directory excluding the size of the subdirectories that exist within that directory. So it basically shows you the total size of all the files that exist in the current directory.

$ du --exculde=mp3
Several times it required to exclude some directory in our size calculation. In such cases the above command would display the size of the current directory along with all its subdirectories, but it would exclude all the files having the given pattern present in their filenames.

'df' - finding the disk free space / disk usage

$ df
Hmmm … now “df” command is really useful, and I guess you are going to use it over time. Typing the above command, outputs a table consisting of 6 columns. All the columns are very easy to understand. Remember that the 'Size', 'Used' and 'Avail' columns use kilobytes as the unit. The 'Use%' column shows the usage as a percentage which is also very useful.

$ df -h
Displays the same output as the previous command but the '-h' indicates human readable format. Hence instead of kilobytes as the unit the output would have 'M' for Megabytes and 'G' for Gigabytes.

Example: Linux installed on /dev/hda1
$ df -h | grep /dev/hda1

All right, this is not the only option to check the sizes and free spaces but there are a few more options that can be used with 'du' and 'df' . I will discuss it later.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c

usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C]
[-s S] [-d] [-ff] [-v V]
positive_seq negative_seq

positional arguments:
positive_seq the fasta file for the positive sequences
negative_seq the fasta file for the negative sequences

Address of the bookmark: https://github.com/yanshen43/MCAT

Address of the bookmark: http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

#!/usr/bin/perl

APPEAL:

listen (please, please);

open yourself, wide;
join (you, me),
connect (us,together),

tell me.

do something if distressed;

@dawn, dance;
@evening, sing;
read (books,$poems,stories) until peaceful;
study if able;

write me if-you-please;

sort your feelings, reset goals, seek (friends, family, anyone);

do*not*die (like this)
if sin abounds;

keys (hidden), open (locks, doors), tell secrets;
do not, I-beg-you, close them, yet.

accept (yourself, changes),
bind (grief, despair);

require truth, goodness if-you-will, each moment;

select (always), length(of-days)

# listen (a perl poem)
# Sharon Hopkins
# rev. June 19, 1995

For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.

http://milkweedgenome.org/?q=scripts

Address of the bookmark: http://milkweedgenome.org/?q=scripts

#Find the reverse complement of a DNA string.
#Given: A DNA string Pattern.
#Return: Pattern, the reverse complement of Pattern.

use strict;
use warnings;

my $string="AAAACCCGGT";
my $finalString="";
my %hash = (
    "C" => "G",
    "A" => "T",
    "T" => "A",
    "G" => "C",
);

for (my $aa=0; $aa<=(length($string)-1); $aa++) {
    my $char=substr $string, $aa, 1;
    #print $hash{$char};
    $finalString="$hash{$char}"."$finalString";
}

print $finalString;
print "\n";