Hi ,
I have a peculiar case, where my sed command is working on a file which contains lines of small length.
sed "s/XYZ:1/XYZ:3/g" abc.txt > xyz.txt
when abc.txt contains lines of small length(currently around 80 chars) , this sed command is working fine.
when abc.txt contains lines of... (3 Replies)
Hi all,
I have a flat file of 1000 rows. I want to check the length of the 5th column. The one having the longest length , I want to set it as DEFINED PARAMETER.
So later I can check others with that particular number only.
Any ideas ?? (2 Replies)
Hi,
This is my first post to this site. So kindly forgive if I am writing in a wrong section.
My query is that...
I want to modify the max username length size. I guess it is 32/64 on CentOS. Now I want to change it to 128. Is there any way to do that?
Thanks in advance!! :) (4 Replies)
Hey Any one...
Do u know any way I can modify the max username length in unix? I guess it is 32/64 characters by default. Suppose I want to increase it to 128.
i hav tried /etc/skel
but no use...
How can I do that? (2 Replies)
I need a way to extract data from
X 4T Solution 21 OCT 2011 37 .00
to account 12345678 User1 user2
X 4T Solution Solution Unlimited 11 Sep 2009 248 .00
to account 87654321 user3 user4
I need it to extract 'X' '37.00' and account number 12345678.
I have extracted above stuff... (3 Replies)
I have a file that stores data in pairs of lines, following this format:
line 1: header (preceded by ">")
line 2: sequence
Example.txt:
>seq1 name
GATTGATGTTTGAGTTTTGGTTTTT
>seq2 name
TTTTCTTC
I want to filter out the sequences and corresponding headers for all sequences that are less... (2 Replies)
Hi all,
I'm struggling to filter my data frame. I need to print only those lines whose max value (the number of columns may vary) is above a cut-off value.
My data looks like this:
chr22 17565753 17565754 5 4 5 5 6 2 5 5 6 2
chr22 17565754 ... (2 Replies)
Hi
Can someone tell me which script will work best (in terms of speed and simplicity to write and run) for a large text file to filter all the lines with a minimum specified length of words ? A sample script with be definitely of great help !!! Thanks in advance. :) (4 Replies)
Hello Team,
Need your expertise on following:
Here is the set of data:
C1|4|C1SP1|A1|C1BP1|T1
C1|4|C1SP2|A1|C1BP2|T2
C2|3|C2SP1|A2|C2BP1|T2
C3|3|C3SP1|A3|C3BP1|T2
C2|2|C2SP2|A2|C2BP2|T1
I need to filter above date base on following two steps:
1. Group them by column 1 and 4
2.... (12 Replies)
Discussion started by: angshuman
12 Replies
LEARN ABOUT DEBIAN
bio::tools::analysis::protein::elm
Bio::Tools::Analysis::Protein::ELM(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::Protein::ELM(3pm)NAME
Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
SYNOPSIS
# get a Bio::Seq object to start with, or a Bio::PrimaryI object.
my $tool = Bio::Tools::Analysis::Protein::ELM->
new(seq => $seqobj->primary_seq() );
$tool->compartment(['ER', 'Golgi']);
$tool->species(9606);
$tool->run;
my @fts = $tool->Result('Bio::SeqFeatureI');
$seqobj->addSeqFeature(@fts);
DESCRIPTION
This module is a wrapper around the ELM server <http://elm.eu.org/> which predicts short functional motifs on amino acid sequences.
False positives can be limited by providing values for the species and cellular compartment of the protein. To set the species attribute,
use either a Bio::Species object or an NCBI taxon ID number. To set the cell compartment attribute (any number of compartments can be
chosen) use an array reference to a list of compartment names.
Results can be obtained either as raw text output, parsed into a data structure, or as Bio::SeqFeature::Generic objects.
SEE ALSO
Bio::SimpleAnalysisI, Bio::WebAgent
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/
AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk,
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
compartment
name : compartment
usage : $elm->compartment(['golgi', 'er']);
purpose : get/setter for cell compartment specifications
arguments : None, single compartment string or ref to array of
compartment names.
returns : Array of compartment names (default if not previously set).
species
name : species
usage : $tool->species('9606');
purpose : get/setter for species selction for ELM server
arguments : none, taxon_id or Bio::Species object
returns : a string of the ncbi taxon_id
result
name : result
usage : $tool->result('Bio::SeqFeatureI');
purpose : parse results into sequence features or basic data format
arguments : 1. none (retrieves raw text without html)
2. a value (retrieves data structure)
3. 'Bio::SeqFeatureI' (returns array of sequence features)
tag names are : {method => 'ELM', motif => motifname,
peptide => seqeunce of match,
concensus => regexp of match}.
returns : see arguments.
perl v5.14.2 2012-03-02 Bio::Tools::Analysis::Protein::ELM(3pm)