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Thanks for this great tool! I just downloaded it and found I had to move cazy_webscraper.py out of the scraper package folder and into the main directory for the script to run.
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@widdowquinn I think I've thought of another way to increase the rate of scraping CAZy
Atm, when parsing a protein (our current working protein):
1. The scraper checks if the protein is already …
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Downloading of significant amounts of data may take some time. If there is an interruption for any reason, the script stops, but none of the gathered data is available to the user. This could be extre…
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Hi Le,
I was wondering what is the running time like for a shotgun sample of about 20 million reads?
It seems taking forever (more than 30 hours at least) even running on 16 threads.
Subsampling …
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The config file approach is great if you want or need to preserve or repeat your query.
If you want a "quick" search (e.g. when testing) then it would be good to have the option to specify options …
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Hi,
Thanks for developing such a great pipeline. Could you provide more explanations about the output files?
I got the following results:
cgc.gff
cgc.out
diamond.out
hmmer.out
Hotpep.out
overv…
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Hi Carlos,
I have a question: my sequences are from Quercus robur, commonly known as common oak, and I got some times GOterms relative to animal species. An example below with the sequence Qrob_P06…
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Hello, I would like to update the dbcan database in dram. From what I understood it's the version 8:
DRAM_data/dbCAN-HMMdb-V8.txt (there is also h3f, h3p h3i and h3m files)
according the dbcan pa…
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Glycosyl transferase, family 14 (IPR003406) corresponds to CAZT GT14 family, which includes several different functional activities, not all of which are acetylglucosaminyltransferases:
http://www.ca…
sjm41 updated
3 years ago
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Description of InterPro "Glycosyl transferase, family 31 (IPR00265)" includes:
_Glycosyltransferase family 31 (GH31) comprises enzymes with a number of known activities; N-acetyllactosaminide beta-…
sjm41 updated
3 years ago