<title> EDAR Gene Sequencing
<dt>Test Code:</dt><dd>156 </dd><dt>Turnaround Time:</dt><dd>6-8 weeks </dd><dt>Preferred Specimen:</dt><dd>2-5 mL Blood - Lavender Top Tube </dd><dt>CPT Codes:</dt><dd>81479x1</dd><ul id="clinical-utility"><li>Confirmation of a clinical diagnosis </li><li>Differentiation between X-linked and autosomal forms of the disease </li><li>Prenatal diagnosis in at-risk pregnancies</li><ol id="references"><li>Bal, E et al. Hum Mutat. 28:703-709, 2007.</li><li>Headon et al. Nature. 414:913-916, 2001.</li><li>Monreal et al. Nat Genet 22:366-369, 1999.</li><li>Chassaing et al. Hum Mutat. 27(3):255-259, 2006</li>
The <…..> are not needed only the text is, if it is possible. Thanks .
hi all,
i have a html file something similar to this.
<tr class="evenrow">
<td class="data">added</td><td class="data">xyz@abc.com</td>
<td class="data">filename.sql</td><td class="modifications-data">08/25/2009 07:58:40</td><td class="data">Added TK prof script</td>
</tr>
<tr... (1 Reply)
Hi!
I have a bunch of HTML files, which I want to parse to CSV files. Every page has a table in it, and I need to parse each row into a csv record.
With awk and sed, I managed to put every table row in separate lines. So my file looks like this:
<TR> .... </TR>
<TR> .... </TR>
...One... (1 Reply)
hi guys,
i want to parse a file using public function, the file contain raw data in the below format i want to get the output like this to load it to Oracle DB
MARWA1,BSS:26,1,3,0,0,0,0,0.00,22,22,22.00
MARWA2,BSS:26,1,3,0,0,0,0,0.00,22,22,22.00
this the file raw format:
Number of... (6 Replies)
Hello,
I have a html file like this :
<html>
...
...
...
<table>
.......
......
</table>
<table name = "hi">
......
.....
...
</table>
<h1> Welcome </h1>
.......
......
</html> (11 Replies)
Hello,
I want to extract some informations from a html (website, http://www.energiecontracting.de/7-mitglieder/von-A-Z.php?a_z=B&seite=2 ) file and save those in a predefined format (.csv).. However it seems that the code on that website is kinda messy and I can't find a way to handle it... (5 Replies)
Hi all, I have a file that contains a good hundred of these job definitions below:
Job Name Last Start Last End ST Run Pri/Xit
________________________________________________________________ ____________________... (7 Replies)
<DIV><P>Pré-condição aceder ao ecrã Home do MRS.</P></DIV><DIV><P>OK.</P></DIV><DIV><P>Seleccionar Pesquisa de Recepção Directa.</P></DIV><DIV><P>Confirmar que abriu ecrã de Recepção Directa.</P></DIV><DIV> (6 Replies)
I have downloaded source code for 97 files using:
wget -x -i link.txt then run a rename loop:
for file in *
do
mv $file $file.txt
done to keep the html tags but make the file a text that can be parsed.
In each of the 97 txt files the gene # is variable, but the gene is associated... (15 Replies)
I downloaded source code using:
wget -qO- http://fulgentdiagnostics.com/test/clinical-exome/ | cat > flugentsource.txt
Now I am trying to use sed to parse it to confirm a gene count. Basically, output (flugent.txt) all the gene names with a total count after them
I'm not all that... (5 Replies)
Hi,
im trying to read a Temperature value from html code.
So far i have managed to reduce the whole html page down to this single line with the following sed command:sed -n '/Temperature/p' $temp_temperature | tee temp_string
<TD width='350'>Temperature :</td><td>25... (2 Replies)
Discussion started by: naittis
2 Replies
LEARN ABOUT DEBIAN
bio::tools::fgenesh
Bio::Tools::Fgenesh(3pm) User Contributed Perl Documentation Bio::Tools::Fgenesh(3pm)NAME
Bio::Tools::Fgenesh - parse results of one Fgenesh run
SYNOPSIS
use Bio::Tools::Fgenesh;
$fgenesh = Bio::Tools::Fgenesh->new(-file => 'result.fgenesh');
# filehandle:
$fgenesh = Bio::Tools::Fgenesh->new( -fh => *INPUT );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same
while($gene = $fgenesh->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
# off Bio::SeqFeature::Gene::Transcript.
#
# $gene->exons() returns an array of
# Bio::Tools::Prediction::Exon objects
# all exons:
@exon_arr = $gene->exons();
# initial exons only
@init_exons = $gene->exons('Initial');
# internal exons only
@intrl_exons = $gene->exons('Internal');
# terminal exons only
@term_exons = $gene->exons('Terminal');
# singleton exons:
($single_exon) = $gene->exons();
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$fgenesh->close();
DESCRIPTION
The Fgenesh module provides a parser for Fgenesh (version 2) gene structure prediction output. It parses one gene prediction into a
Bio::SeqFeature::Gene::Transcript- derived object.
This module also implements the Bio::SeqAnalysisParserI interface, and thus can be used wherever such an object fits.
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 - Chris Dwan
Email chris-at-dwan.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
analysis_method
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/genscan/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($gene = $fgenesh->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Fgenesh result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
next_prediction
Title : next_prediction
Usage : while($gene = $fgenesh->next_prediction()) { ... }
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
_parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
_prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($gene)
Function: internal
Example :
Returns :
_predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
_has_cds
Title : _has_cds()
Usage : $obj->_has_cds()
Function: Whether or not the result contains the predicted CDSs, too.
Example :
Returns : TRUE or FALSE
_read_fasta_seq
Title : _read_fasta_seq()
Usage : ($id,$seqstr) = $obj->_read_fasta_seq();
Function: Simple but specialised FASTA format sequence reader. Uses
$self->_readline() to retrieve input, and is able to strip off
the traling description lines.
Example :
Returns : An array of two elements: fasta_id & sequence
perl v5.14.2 2012-03-02 Bio::Tools::Fgenesh(3pm)