Hi all,
I have a script below which meant to decompress *.tr.gz to allocated folder.
e.g. hello.tar.gz should be decompress to a subdirectory called hello and all the files should be in hello subdirectory.
How do i do it? Am i missing anything?
Condition: there are existing tar.gz in teh... (3 Replies)
Hi All,
I am trying to rsync some of the latest files from remote m/c to my local linux box.
Folder structure in my remote m/c looks like this
/pub/Nightly/Package/ROLL/WIN
/pub/Nightly/Package/SOLL/sol
/pub/Nightly/Package/SOLL/linux
Each of the folder contains gzip files which on daily... (0 Replies)
I want a mechanism to monitor a folder full of files that are sensitive. I want to log all accesses,modifications and changes to any file within the folder in a log file which should give me access/modify/change times,the user id of the process which tried and the pid.
Even some idea of what to... (1 Reply)
Hi,
This evening i would like to download multiple pcap captures files in the wireshark wiki sites. My aim is to download the capture files .pcap .cap and etc on the wireshark site SampleCaptures - The Wireshark Wiki. i already used wget, lynx, htget but still their problem downloading..it seems... (1 Reply)
hi,
i have a requirement to delete all the files from all the directories except some specific directories like archive and log.
for example:
there are following directories such as
A B C D Archive E Log F
which contains some sub directories and files. The requirement is to delete all the... (7 Replies)
The bash below will download all the files in download to /home/Desktop/folder. That works great, but within /home/Desktop/folder there are several folders bam, other, and vcf, is there a way to specify by extention in the download file where to download it to?
For example, all .pdf and .zip... (2 Replies)
I have a directory /home/cmccabe/nfs/exportedReports that contains multiple folders in it. The find writes the name of each folder to out.txt. A new directory is then created in a new location /home/cmccabe/Desktop/NGS/API, named with the date. What I am trying to do, unsuccessfully at the moment,... (7 Replies)
The below bash is trying to list the folders in a specific directory. It seems close but adds the path to the filename, which basename could strip off I think, but not sure why it writes the text file created? This list of folders in the directory will be used later, but needs to only be the... (5 Replies)
Hello, how in bash i can get directory loop, but only choose those folders with specific word in it, so it will only echo those with specific word
#!/bin/bash
for filename in /home/test/*
do
if ; then
echo $filename;
fithx! (4 Replies)
Hi Team,
I am new to the linux commands and I really need help . I would be really thankful if I can get some inputs.
I have below folders in the path "/home/temp"
20170428
20170427
20170429
changes
tempI need to get the files generated in the last 15 mins in all the above folders... (4 Replies)
Discussion started by: JackJinu
4 Replies
LEARN ABOUT DEBIAN
bio::tools::run::samtools
Bio::Tools::Run::Samtools(3pm) User Contributed Perl Documentation Bio::Tools::Run::Samtools(3pm)NAME
Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*
SYNOPSIS
# convert a sam to a bam
$samt = Bio::Tools::Run::Samtools( -command => 'view',
-sam_input => 1,
-bam_output => 1 );
$samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
# sort it
$samt = Bio::Tools::Run::Samtools( -command => 'sort' );
$samt->run( -bam => "mysam.bam", -pfx => "mysam.srt" );
# now create an assembly
$assy = Bio::IO::Assembly->new( -file => "mysam.srt.bam",
-refdb => "myref.fas" );
DESCRIPTION
This is a wrapper for running samtools, a suite of large-alignment reading and manipulation programs available at
<http://samtools.sourceforge.net/>.
RUNNING COMMANDS
To run a "samtools" command, construct a run factory, specifying the desired command using the "-command" argument in the factory
constructor, along with options specific to that command (see "OPTIONS"):
$samt = Bio::Tools::Run::Samtools->new( -command => 'view',
-sam_input => 1,
-bam_output => 1);
To execute, use the "run()" method. Input and output files are specified in the arguments of "run()" (see "FILES"):
$samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
OPTIONS
"samtools" is complex, with many subprograms (commands) and command-line options and file specs for each. This module attempts to provide
commands and options comprehensively. You can browse the choices like so:
$samt = Bio::Tools::Run::Samtools->new( -command => 'pileup' );
# all samtools commands
@all_commands = $samt->available_parameters('commands');
@all_commands = $samt->available_commands; # alias
# just for pileup
@pup_params = $samt->available_parameters('params');
@pup_switches = $samt->available_parameters('switches');
@pup_all_options = $samt->available_parameters();
Reasonably mnemonic names have been assigned to the single-letter command line options. These are the names returned by
"available_parameters", and can be used in the factory constructor like typical BioPerl named parameters.
See <http://samtools.sourceforge.net/samtools.shtml> for the gory details.
FILES
When a command requires filenames, these are provided to the "run()" method, not the constructor ("new()"). To see the set of files
required by a command, use "available_parameters('filespec')" or the alias "filespec()":
$samt = Bio::Tools::Run::Samtools->new( -command => 'view' );
@filespec = $samt->filespec;
This example returns the following array:
bam
>out
This indicates that the bam/sam file (bam) and the output file (out) MUST be specified in the "run()" argument list:
$samt->run( -bam => 'mysam.sam', -out => 'mysam.cvt' );
If files are not specified per the filespec, text sent to STDOUT and STDERR is saved and is accessible with "$bwafac-"stdout()> and
"$bwafac-"stderr()>.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = new Bio::Tools::Run::Samtools();
Function: Builds a new Bio::Tools::Run::Samtools object
Returns : an instance of Bio::Tools::Run::Samtools
Args :
perl v5.12.3 2011-06-18 Bio::Tools::Run::Samtools(3pm)