I have many messages such as the test message below:
00:00000:00021:2002/05/13 13:57:00.51 ERROR:- Test error, my test error!!!
I am writing a script in which I need to get everything from the word "ERROR:-" onwards.
I normally use awk for these things, but I am not an expert at it so i am... (6 Replies)
Hi,
I know sed is stream text editor and not a bit more than that. Can anyone explain its usage and advantages?
How is awk different from sed?
I donno i am a bit confused about it. But i have coded in awk and shell.
Thanks,
Nisha
:confused: (7 Replies)
Hey all,
Can I put sed command inside the awk action ?? If not then can i do grep in the awk action ??
For ex:
awk '$1=="174" { ppid=($2) ; sed -n '/$ppid/p' tempfind.txt ; }' tempfind.txt
Assume: 174 is string.
Assume: tempfind.txt is used for awk and sed both.
tempfind.txt... (11 Replies)
Hi,
I have a data file with 5 columns - like this:
"20080401 09:43:08.770798 +0100s","TEST 1","R 1","A TEST","Nov 27 2007","1"
"20080401 09:43:08.770798 +0100s","THIS IS A TEST","R 2","B TEST","Nov 30 2007","10"
"20080401 09:43:08.770798 +0100s","ANOTHER TEST","R 3","B TEST","Nov 05... (7 Replies)
I've got an inventory database with eight columns with things like product name, manufacturer, UPC code, etc. on each line. Our PO (purchase order) number is in the first column. I can grep the date and get the full line of data but I would like to strip out everything but the PO number in the... (5 Replies)
What if I wanted to add a word such as IT after the first character and if theres 3 characters, after the 2nd character?
output would be:
G, it H
G, H it P
G, H, P it L
I'm thinking that AWK would be the easiest way to do this... Currently looking it up.
Right now I'm using awk but I... (13 Replies)
Hi All,
Is there a way of comparing two columns in the same file and deleting the row if the values of the columns match.
I have the sample data file as below.
M024900|175309.00|968.00|17
M025001|19861.79|97.90|148
M025002|431.70|159.00|3
M025003|912.30|159.90|6 ... (6 Replies)
I have a file that contain the data below:
B1
1
2
3
B2
20
30
40
B3
7
8
B4
100
B5
21
22
23How can I retrieve the data for B1 into a seperate file. (8 Replies)
Dear Geeks,
I want to manipulate a file with certain modifications for that using sed or AWK how to do this process for one file i have this type of data.
Input File:
"Restricted and Reserved names .ANISH",3798,"TEST.CO",1201208,6/16/10 0:00,6/16/13 0:00,,,"CO","2nd"^M
"Restricted and... (4 Replies)
Hi,
I am running a script sample.sh in bash environment .In the script i am using sed and awk commands which when executed individually from terminal they are getting executed normally but when i give these sed and awk commands in the script it is giving the below errors :-
./sample.sh: line... (12 Replies)
Discussion started by: satishmallidi
12 Replies
LEARN ABOUT DEBIAN
bio::matrix::psm::instancesitei
Bio::Matrix::PSM::InstanceSiteI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::InstanceSiteI(3pm)NAME
Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
SYNOPSIS
use Bio::Matrix::PSM::InstanceSite;
#Y ou can get an InstanceSite object either from a file:
my ($instances,$matrix)=$SomePSMFile->parse_next;
#or from memory
my %params=(seq => 'TATAAT',
id => "TATAbox1",
accession => 'ENSG00000122304',
mid => 'TB1',
desc => 'TATA box, experimentally verified in PRM1 gene',
relpos => -35);
DESCRIPTION
Abstract interface to PSM site occurrence (PSM sequence match). InstanceSite objects may be used to describe a PSM (See
Bio::Matrix::PSM::SiteMatrix) sequence matches. The usual characteristic of such a match is sequence coordinates, score, sequence and
sequence (gene) identifier- accession number or other id. This object inherits from Bio::LocatableSeq (which defines the real sequence) and
might hold a SiteMatrix object, used to detect the CRE (cis-regulatory element), or created from this CRE. While the documentation states
that the motif id and gene id (accession) combination should be unique, this is not entirely true- there might be more than one occurrence
of the same cis-regulatory element in the upstream region of the same gene. Therefore relpos would be the third element to create a really
unique combination.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan Kirov
Email skirov@utk.edu
SEE ALSO
Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::IO
APPENDIX
mid
Title : mid
Usage : my $mid=$instance->mid;
Function: Get/Set the motif id
Throws :
Returns : scalar
Args : scalar
score
Title : score
Usage : my $score=$instance->score;
Function: Get/Set the score (mismatches) between the instance and the attached (or
initial) PSM
Throws :
Returns : real number
Args : real number
start
Title : start
Usage : my $start=$instance->start;
Function: Get/Set the position of the instance on the sequence used
Throws :
Returns : integer
Args : integer
relpos
Title : relpos
Usage : my $seqpos=$instance->relpos;
Function: Get/Set the relative position of the instance with respect to the transcription start
site (if known). Can and usually is negative.
Throws :
Returns : integer
Args : integer
minstance
Title : minstance
Usage : my $minstance=$misntance->score;
Function: Get/Set the unique identifier- sequence id/motif id, for example PRM1_TATAbox.
Not necessarily human readable.
Throws :
Returns : string
Args : string
perl v5.14.2 2012-03-02 Bio::Matrix::PSM::InstanceSiteI(3pm)