reading information from a table and apply a command on multiple files
Hey gyuz,
I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :
This will store all the reads from given bam file within the region of interest in region1.txt
Now I have several bam files and several regions for each which are different. (regions are not the same in all bam files)
I prepared a list of them like below:
bam1 region1
bam1 region2
bam1 region3
bam2 region4
bam2 region4
bam3 region5
I want the script to read from the table and apply the function on proper bam file and regions and report the output for each region in a single file. region1.txt, region2.txt, region3.txt,.....
If you can help me with this you saved my time so much!!
Hi all,
Can you please help me in this aspect. I devoloped a FTP script to copy a directory to remote server. Now i got stuck-up in changing the file permissions for all the files in directory. I tried to change the permissions of single file and I did it but failed in changing... (3 Replies)
Hi everyone!!
I have a database table, which has file_name as one of its fields.
Example:
File_ID File_Name Directory Size
0001 UNO_1232 /apps/opt 234
0002 UNO_1234 /apps/opt 788
0003 UNO_1235 /apps/opt 897
0004 UNO_1236 /apps/opt 568
I have to... (3 Replies)
Hi All,
I am using the awk command to replace ',' by '\t' (tabs) in a csv file. I would like to apply this to all .csv files in a directory and create .txt files with the tabs.
How would I do this in a script?
I have the following script called "csvtabs":
awk 'BEGIN {
FS... (4 Replies)
Hi,
I have a bunch of records within a directory where each one has this form:
(example file1)
1 2 50 90 80 90 43512 98 0909 79869 -9 7878 33222 8787 9090 89898 7878 8989 7878 6767 89 89 78676 9898 000 7878 5656 5454 5454
and i want for all of these files to be... (3 Replies)
Hello there,
I am trying to extract (string) information ( a list words) from 4 files and then put the results into 1 file. Currently I am doing this using grep -f list.txt file1 . and repeat the process for the other 3 files. The reasons i am doing that (a) I do know how to code (b) each file... (4 Replies)
Hi ,
I have searched through the forum but not able to find out any help :(
i have a directory having lot of files which contains sql statemtns
eg : file 1 contains
select from table_name1 where .....................
select from
table_name2 where ..........
select
from ... (3 Replies)
hi everyone,
im stuck in here with shell :) can you help me??
i have a directory with alot files (genbank files ... all ended in .gbk ) more than 1000 for sure ... and i want to read each one of them and search for some information and if i found the right one i save in new file with new... (6 Replies)
Hi,
I need to load data from two files to a single table.
My requirement is that I get two files in which a few column data are manadatory.
These files are identified based on the file name.
For example, I have two files ABCFile and BCDFile. ABCFile has mandatory data in column 3 and 4... (0 Replies)
Hi all!
I have this command
grep -E '^\To: |^\Date: |^\Subject: ' fileA.txt > fileA_1.txt && grep -v '^\To: |^\Date: |^\Subject: ' fileA.txt >> fileA_1.txt && rm fileA.txt && sed -i -e 's/\(Date: \|Subject: \|To: \)//g' fileA_1.txtHow do I apply it to all the files in the folder (each file has a... (7 Replies)
Hi ,
Can any please help the below requirement on all multiple servers and multiple dbs.
update configuration set value='yes' ;1)
the above statement apply on 31 Databases at a time on different Ip address
eg : 10.104.1.12 (unix ip address )
the above ip box contains 4 db's eg : db... (2 Replies)
Discussion started by: venkat918
2 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)