awk to parse html file Post: 302919224

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Top Forums Shell Programming and Scripting awk to parse html file Post 302919224 by Don Cragun on Monday 29th of September 2014 03:47:15 PM

09-29-2014

Registered User

In cases where you don't have quoted > characters in tags (and I didn't see any of them in your samples, but didn't do an exhaustive search in your attachment), the following much simpler script might work:

Code:

awk -F '<[^>]*>' '{$1=$1}1' OFS='' file

With the sample data you posted in the 1st message in this thread, it produces the output:

Code:

 EDAR Gene Sequencing
Test Code:
    156 
 
    Turnaround Time:
    6-8 weeks 
 
    Preferred Specimen:
    2-5 mL Blood - Lavender Top Tube 
 
CPT Codes:
    81479x1
 

    Confirmation of a clinical diagnosis 
    Differentiation between X-linked and autosomal forms of the disease 
    Prenatal diagnosis in at-risk pregnancies
 

    Bal, E et al. Hum Mutat. 28:703-709, 2007.
    Headon et al. Nature. 414:913-916, 2001.
    Monreal et al. Nat Genet 22:366-369, 1999.
    Chassaing et al. Hum Mutat. 27(3):255-259, 2006

I didn't see any problems processing your attached sample either, but due to the length (since this preserves all input lines and just removes tags), I won't post the results here. It would also be easy to get rid of empty lines after removing tags if that is what you want.

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LEARN ABOUT DEBIAN

bio::seqfeature::gene::nc_feature

Bio::SeqFeature::Gene::NC_Feature(3pm)			User Contributed Perl Documentation		    Bio::SeqFeature::Gene::NC_Feature(3pm)

NAME

       Bio::SeqFeature::Gene::NC_Feature.pm - superclass for non-coding features

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - David Block
       Email dblock@gnf.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   is_coding
	Title	: is_coding
	Usage	: if ($feature->is_coding()) {
			    #do something
		   }
	Function: Whether or not the feature codes for amino acid.
	Returns : FALSE
	Args	: none

   cds
	Title	: cds
	Usage	: $cds=$feature->cds();
	Function: get the coding sequence of this feature
	Returns : undef
	Args	: none

perl v5.14.2							    2012-03-02				    Bio::SeqFeature::Gene::NC_Feature(3pm)