create_cazy_db fails

[lonsbio]

Unable to create database on Python 2.7.13. Output (exlcucing BeautifulSoup warning) as follows:

>> Gathering species codes for species with full genomes
>> Glycoside-Hydrolases
>> 145 families found on http://www.cazy.org/Glycoside-Hydrolases.html
> GH1

then error

first_page_idx = int(page_index_list[0]['href'].split('PRINC=')[-1].split('#')[0]) # be careful with this
ValueError: invalid literal for int() with base 10: 'GH1_archaea.html?debut_TAXO=100'

Has the pagination code changed for the expression to fail?

[rvhonorato]

Yes, looks like the pagination changed a bit. I did a quick fix using regular expressions #5 and it should work fine now. Thanks for opening this issue.

[lonsbio]

Thanks! I tried my own patch overnight (not as elegant) and it seemed to work too.

Also, I'm not sure if this is a recent issue or incidental. My DB download file seems to have newlines surrounding the organism field:

domain	protein_name	family	tag	organism_code	ec	genbank	uniprot	subfamily	organism	pdb
	 Ahos_0285	GH1		invalid	 	AEE93176.1	 		
Acidianus hospitalis W1
	  

Fixing it does't seem to effect the extract script, but does make the csv (tsv) file readable. Is the wrapping intentional?