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Frost-group / Nornour

An open-source project in computational modelling and design of antimicrobrial and anticancer peptides.
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Curate an initial peptide database #1

Open jarvist opened 3 days ago

jarvist commented 3 days ago

https://github.com/Frost-group/Nornour/blob/067016bd4aef46746e1a12cb2dad012116e996e2/0003-DRAMP-database/download.sh

# The DRAMP database offers perfectly formatted downloads of the data
# http://dramp.cpu-bioinfor.org/downloads/
#
# *Citation*:
# Shi G, Kang X, Dong F, Liu Y, Zhu N, Hu Y, Xu H, Lao X, Zheng H. DRAMP 3.0:
# an enhanced comprehensive data repository of antimicrobial peptides. Nucleic
# Acids Res. 2022 Jan 7;50(D1):D488-D496. PMID: 34390348

# (づ ᴗ _ ᴗ) づ ♡ - I love a good simple URL download
# wget "http://dramp.cpu-bioinfor.org/downloads/download.php?filename=download_data/DRAMP3.0_new/Antibacterial_amps.txt" -O Antibacterial_amps.txt
jarvist commented 3 days ago

Nb: Data still quite unclean! '24..spacerO()hxwlUgimvfJyqtZ' characters all turning up

jarvist commented 3 days ago

OK, this is now ready to use with a LSTM etc.; such as this super slick Javascript interface: https://cs.stanford.edu/people/karpathy/recurrentjs/

jarvist commented 1 day ago

& the RW Lexicon dataset from the paper added: https://github.com/Frost-group/Nornour/blob/0c92669f98355e71841e7aaf7adf86361cdf4575/0003b-RW-Lexicon/download.sh#L1-L8

KamDB commented 1 day ago

completed