<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::asn1::entrezgene::indexer
Bio::ASN1::EntrezGene::Indexer(3pm) User Contributed Perl Documentation Bio::ASN1::EntrezGene::Indexer(3pm)NAME
Bio::ASN1::EntrezGene::Indexer - Indexes NCBI Entrez Gene files.
SYNOPSIS
use Bio::ASN1::EntrezGene::Indexer;
# creating & using the index is just a few lines
my $inx = Bio::ASN1::EntrezGene::Indexer->new(
-filename => 'entrezgene.idx',
-write_flag => 'WRITE'); # needed for make_index call, but if opening
# existing index file, don't set write flag!
$inx->make_index('Homo_sapiens', 'Mus_musculus', 'Rattus_norvegicus');
my $seq = $inx->fetch(10); # Bio::Seq obj for Entrez Gene #10
# alternatively, if one prefers just a data structure instead of objects
$seq = $inx->fetch_hash(10); # a hash produced by Bio::ASN1::EntrezGene
# that contains all data in the Entrez Gene record
# note that in case you wonder, you can get the files 'Homo_sapiens'
# from NCBI Entrez Gene ftp download, DATA/ASN/Mammalia directory
PREREQUISITE
Bio::ASN1::EntrezGene, Bioperl version that contains Stefan Kirov's entrezgene.pm and all dependencies therein.
INSTALLATION
Same as Bio::ASN1::EntrezGene
DESCRIPTION
Bio::ASN1::EntrezGene::Indexer is a Perl Indexer for NCBI Entrez Gene genome databases. It processes an ASN.1-formatted Entrez Gene record
and stores the file position for each record in a way compliant with Bioperl standard (in fact its a subclass of Bioperl's index objects).
Note that this module does not parse record, because it needs to run fast and grab only the gene ids. For parsing record, use
Bio::ASN1::EntrezGene, or better yet, use Bio::SeqIO, format 'entrezgene'.
It takes this module (version 1.07) 21 seconds to index the human genome Entrez Gene file (Apr. 5/2005 download) on one 2.4 GHz Intel Xeon
processor.
SEE ALSO
For details on various parsers I generated for Entrez Gene, example scripts that uses/benchmarks the modules, please see
<http://sourceforge.net/projects/egparser/>. Those other parsers etc. are included in V1.05 download.
AUTHOR
Dr. Mingyi Liu <mingyi.liu@gpc-biotech.com>
COPYRIGHT
The Bio::ASN1::EntrezGene module and its related modules and scripts are copyright (c) 2005 Mingyi Liu, GPC Biotech AG and Altana Research
Institute. All rights reserved. I created these modules when working on a collaboration project between these two companies. Therefore a
special thanks for the two companies to allow the release of the code into public domain.
You may use and distribute them under the terms of the Perl itself or GPL (<http://www.gnu.org/copyleft/gpl.html>).
CITATION
Liu, M and Grigoriev, A(2005) "Fast Parsers for Entrez Gene" Bioinformatics. In press
OPERATION SYSTEMS SUPPORTED
Any OS that Perl & Bioperl run on.
METHODS
fetch
Parameters: $geneid - id for the Entrez Gene record to be retrieved
Example: my $hash = $indexer->fetch(10); # get Entrez Gene #10
Function: fetch the data for the given Entrez Gene id.
Returns: A Bio::Seq object produced by Bio::SeqIO::entrezgene
Notes: One needs to have Bio::SeqIO::entrezgene installed before
calling this function!
fetch_hash
Parameters: $geneid - id for the Entrez Gene record to be retrieved
Example: my $hash = $indexer->fetch_hash(10); # get Entrez Gene #10
Function: fetch a hash produced by Bio::ASN1::EntrezGene for given Entrez
Gene id.
Returns: A data structure containing all data items from the Entrez
Gene record.
Notes: Alternative to fetch()
_file_handle
Title : _file_handle
Usage : $fh = $index->_file_handle( INT )
Function: Returns an open filehandle for the file
index INT. On opening a new filehandle it
caches it in the @{$index->_filehandle} array.
If the requested filehandle is already open,
it simply returns it from the array.
Example : $fist_file_indexed = $index->_file_handle( 0 );
Returns : ref to a filehandle
Args : INT
Notes : This function is copied from Bio::Index::Abstract. Once that module
changes file handle code like I do below to fit perl 5.005_03, this
sub would be removed from this module
perl v5.14.2 2005-05-04 Bio::ASN1::EntrezGene::Indexer(3pm)