How to insert a string and variable at specified position in command in bash?
I currently have a loop that reads all .bam files in a directory (wont always be 4 like in this example,
into $id. What I am trying to do, unsucessfully, is create specific new lines in an exsisting command using
each $id. Each new line would be:
Tried
directory
standard command
desired command
Last edited by cmccabe; 12-15-2019 at 11:08 AM..
Reason: fixed format
I need a script for...
how to find a position of column data and print some string in the next line and same position
position should find based on *HEADER8* in text
for ex: ord123 abs 123 987HEADER89 test234
ord124 abc 124 987HEADER88 test235
... (1 Reply)
Hi, guys. I have one question:
How can I search for a line with certain string in it and then insert a string into this line?
For example:
There is a file called shadow, the contents of it are below:
**************************
...
yuanz:VIRADxMsadfDF/Q:0:0:50:7:::... (9 Replies)
I want to instert Category:XXXXX into the 2. line
something like this should work, but I have somewhere the wrong sytanx. something with the linebreak goes wrong:
sed "2i\\${n}Category:$cat\n"
Sample:
Titel Blahh Blahh abllk sdhsd sjdhf
Blahh Blah Blahh
Blahh
Should look like... (2 Replies)
I know this script is crummy, but I was just messing around.. how do I get sed's insert command to allow variable expansion to show the filename?
#!/bin/bash
filename=`echo $0`
/usr/bin/sed '/#include/ {
i\
the filename is `$filename`
}' $1
exit 0 (8 Replies)
here is what i want to achieve... consider a file contains below contents. the file size is large about 60mb
cat dump.sql
INSERT INTO `table1` (`id`, `action`, `date`, `descrip`, `lastModified`) VALUES (1,'Change','2011-05-05 00:00:00','Account Updated','2012-02-10... (10 Replies)
Dear all,
i am having text file like below
surya
rama
ranga
laxman
rajesh
reddy
i want add string (OK) before a text from line 3 to 5
the result will be
surya
rama
OK ranga
OK laxman
OK rajesh
reddy (1 Reply)
hi guys,
i want command or script to display the content of file from 2nd position to last but one position of a file
abcdefghdasdasdsd
123,345,678,345,323
434,656,656,656,656
678,878,878,989,545
4565656667,65656
i want to display the same above file without first and... (2 Replies)
Hi,
I have a file with multiple lines(fixed width dat file). I want to search for '02' in the positions 45-46 and if available, in that lines, I need to replace value in position 359 with blank. As I am new to unix, I am not able to figure out how to do this. Can you please help me to achieve... (9 Replies)
hi all
i have a problem in the bash shell. i'd like insert in a variable a file for example :
i have a file datafine.log in this file there is :
17/JUN/2019
i want to insert the value of datafine.log in a variable.
Regards
Frncesco
edit by bakunin: please use CODE-tags for your data... (2 Replies)
I have multiple xml files where i want to update a subnode if the subnode project points to different project or insert a subnode if it doesn't exist using a xmlstarlet or any other command that can be used in a bash script.
I have been able to update the subnode project if it doesn't point to... (1 Reply)
Discussion started by: Sekhar419
1 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)