ls -1tr | head -1
databasefiles_DB_r8n64lfn_11112_20120317
But what if I have more than one old file as below? Your command would give me the single oldest file, but in my situation I have bunch of old files as shown below. If I run the script today (Mar 19), I want to remove all the files created on Mar 17. Please see below.
Thanks again.
Last edited by methyl; 03-19-2012 at 02:28 PM..
Reason: Code tags & some line-up
Hi,
I have a script that works on a unix box but am trying to get it working on a linux box that uses shell. I am not a programmer so this is proving harder than I imagined. I made some changes and ended up with the script below but when I run it I get the following messages. Any help would be... (4 Replies)
Hi,
I am writing a shell script that needs to remove duplicate lines within a file by category.
example:
section a
a
c
b
a
section b
a
b
a
c
I need to remove the duplicates within th category with out removing the duplicates from the 2 different sections (one of the a's in section... (1 Reply)
Hello Folks,
I want to get the results from a SQL query which needs to be exported to a .txt file.
My Script is something like
#!/bin/ksh
db2 connect to DATABASE user user_name using pwd;
touch test.txt
isResult=0;
isResult= `db2 -x select 'ABC',COL_B from TABLE_A WHERE COL_B=CONDITION`... (6 Replies)
Hi,
I am pasring a file line by line. I need to check each field in line and remove particular line.
input file lines are,
02;ABC;PQR
03;aaa;rrr
04;ABC;ggg
09;eee;ABC
04;lmn;stu
I am looking for line containing "ABC" as field value. Now How can I remove this line from input file... (7 Replies)
How can I remove all data that contain domain e.g zzgh@something.com, sdd@something.com.my and gg@something.my in one file? so that i only have data without the domain in the file.
Here is the file structure "test.out"
more test.out
1 zzztop@b.com
1 zzzulll
1 zzzullll@s.com.my
... (4 Replies)
How can i remove a file using shell script when its size exceeds 10MB. Given that file is located in different location to the shell script where it is running? (4 Replies)
Hi All,
I've a csv file in which the record is getting break into 1 line or more than one line. I want to combine those splits into one line and remove the unwanted character existing in the record i.e. double quote symbol ("). The line gets break only when the record contains double... (4 Replies)
hi i need shell scrip to pick the oldest file...
i.e i need a script to pick the oldest file
I had input files in my input folder that are created on saturday,monday,tuesday .. i want a script such that first the script should pick saturday file ,then monday and then file created on... (5 Replies)
I have below file. I want to remove space at begining of every line and then after also remove blank line from file.
I use below code for each operation.
sed -e 's/^*//' < check.txt > check1.txt
sed '/^\s*$/d' < check1.txt > check2.txt
above code not remove all the space... (12 Replies)
Discussion started by: Mohin Jain
12 Replies
LEARN ABOUT DEBIAN
bio::tools::run::alignment::dba
Bio::Tools::Run::Alignment::DBA(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::DBA(3pm)NAME
Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA Block Aligner program.
SYNOPSIS
use Bio::Tools::Run::Alignment::DBA;
# Build a dba alignment factory
my @params = ('matchA' => 0.75,
'matchB' => '0.55',
'dymem' =>'linear');
my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
# Pass the factory a filename with 2 sequences to be aligned.
$inputfilename = 't/data/dbaseq.fa';
# @hsps is an array of GenericHSP objects
my @hsps = $factory->align($inputfilename);
# or
my @files = ('t/data/dbaseq1.fa','t/data/dbaseq2.fa');
my @hsps = $factory->align(@files);
# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = @seq_array;
my @hsps = $factory->align($seq_array_ref);
DESCRIPTION
DNA Block Aligner program (DBA) was developed by Ewan Birney. DBA is part of the Wise package available at
<http://www.sanger.ac.uk/software/wise2>.
You will need to enable dba to find the dba program. This can be done in a few different ways:
1. Define an environmental variable WISEDIR:
export WISEDIR =/usr/local/share/wise2.2.0
2. Include a definition of an environmental variable WISEDIR in every script that will use DBA.pm:
$ENV{WISEDIR} = '/usr/local/share/wise2.2.20';
3. Make sure that the dba application is in your PATH.
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 one
of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
align
Title : align
Usage :
$inputfilename = 't/data/seq.fa';
@hsps = $factory->align($inputfilename);
or
#@seq_array is array of Seq objs
$seq_array_ref = @seq_array;
@hsps = $factory->align($seq_array_ref);
or
my @files = ('t/data/seq1.fa','t/data/seq2.fa');
@hsps = $factory->align(@files);
Function: Perform a DBA alignment
Returns : An array of Bio::Search::HSP::GenericHSP objects
Args : Name of a file containing a set of 2 fasta sequences
or else a reference to an array to 2 Bio::Seq objects.
or else a reference to an array of 2 file
names containing 1 fasta sequence each
Throws an exception if argument is not either a string (eg a
filename) or a reference to an array of 2 Bio::Seq objects. If
argument is string, throws exception if file corresponding to string
name can not be found. If argument is Bio::Seq array, throws
exception if less than two sequence objects are in array.
_run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to dba program
Example :
Returns : nothing; dba output is written to a temp file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to dba
_parse_results
Title : __parse_results
Usage : Internal function, not to be called directly
Function: Parses dba output
Example :
Returns : an reference to an array of GenericHSPs
Args : the name of the output file
_setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for dba program
Example :
Returns : name of file containing dba data input
Args : Seq or Align object reference or input file name
_setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for dba program
Example :
Returns : parameter string to be passed to dba
during align or profile_align
Args : name of calling object
_query_seq()
Title : _query_seq
Usage : Internal function, not to be called directly
Function: get/set for the query sequence
Example :
Returns :
Args :
_subject_seq()
Title : _subject_seq
Usage : Internal function, not to be called directly
Function: get/set for the subject sequence
Example :
Returns :
Args :
perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::DBA(3pm)