how can i extract information from the HTML code

Question

This code is a Single line of .html file which is extracted from the HTML file with a unique identifier "|Rv0153c|":

<TR><TD><small style=font-family:courier> >M. tuberculosis H37Rv|Rv0153c|ptbB<br />MAVRELPGAWNFRDVADTATALRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSRE<br />VARRGPGRVPDGIDVHLLPFPDLADDDADDSAPHETAFKRLLTNDGSNGESGESSQSIND<br />AATRYMTDEYRQFPTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVALVLEAVGL<br />DRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELAPEVVTFTKARLSDGVLGVRAEYLA<br />AARQTIDETYGSLGGYLRDAGISQATVNRMRGVLLG<br /></small><TR><td><b><big>Blastp: <a href="http://tuberculist.epfl.ch/blast_output/Rv0153c.fasta.out"> Pre-computed results</a></big></b><TR><td><b><big>TransMembrane prediction using Hidden Markov Models: <a href="http://tuberculist.epfl.ch/tmhmm/Rv0153c.html"> TMHMM</a></big></b><base target="_blank"/><TR><td><b><big>Genomic sequence</big></b><br /><br /><form action="dnaseq.php" method="get">

i want to write a code which is able to extract the given information(given below) in a given format from this line of .html code:

>M. tuberculosis H37Rv|Rv0153c|ptbB
MAVRELPGAWNFRDVADTATALRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSRE
VARRGPGRVPDGIDVHLLPFPDLADDDADDSAPHETAFKRLLTNDGSNGESGESSQSIND
AATRYMTDEYRQFPTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVALVLEAVGL
DRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELAPEVVTFTKARLSDGVLGVRAEYLA
AARQTIDETYGSLGGYLRDAGISQATVNRMRGVLLG

you should probably check out regular expressions. Python has an re module which can handle this for you. — Chris Hawkes
– Chris Hawkes, Commented Oct 23, 2013 at 14:14

mrlouhibi · Accepted Answer · 2013-10-23 14:47:51Z

1

I think that what you are looking for is an HTML parser: Simple HTML and XHTML parser

answered Oct 23, 2013 at 14:47

mrlouhibi

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JAZs Over a year ago

thanks for your valuable suggestion HTML parser is great for my work just 3 line code can be able to do exactly what i was looking for.

Venkateshwaran Selvaraj · Accepted Answer · 2013-10-23 17:24:44Z

1

You can use Python and regular expression library.

from bs4 import BeautifulSoup
import re
sentence = '<TR><TD><small style=font-family:courier> >M. tuberculosis H37Rv|Rv0153c|ptbB<br />MAVRELPGAWNFRDVADTATALRPGRLFRSSELSRLDDAGRATLRRLGITDVADLRSSRE<br />VARRGPGRVPDGIDVHLLPFPDLADDDADDSAPHETAFKRLLTNDGSNGESGESSQSIND<br />AATRYMTDEYRQFPTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVALVLEAVGL<br />DRDVIVADYLRSNDSVPQLRARISEMIQQRFDTELAPEVVTFTKARLSDGVLGVRAEYLA<br />AARQTIDETYGSLGGYLRDAGISQATVNRMRGVLLG<br /></small><TR><td><b><big>Blastp: <a href="http://tuberculist.epfl.ch/blast_output/Rv0153c.fasta.out"> Pre-computed results</a></big></b><TR><td><b><big>TransMembrane prediction using Hidden Markov Models: <a href="http://tuberculist.epfl.ch/tmhmm/Rv0153c.html"> TMHMM</a></big></b><base target="_blank"/><TR><td><b><big>Genomic sequence</big></b><br /><br /><form action="dnaseq.php" method="get">'   
print re.sub('<[^>]*>', '',  sentence)

HTH.

edited Oct 23, 2013 at 17:24

answered Oct 23, 2013 at 17:06

Venkateshwaran Selvaraj

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1 Comment

DSM Over a year ago

You're not actually using BeautifulSoup here, you're merely using a regex.

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