<commit_before>#!/usr/bin/env bash
# Please be advised that files downloaded using this script are subject of different licencing policies
# and use of some files may be forbidden for commercial purposes. Authors of some files ask for citation
# if you use their work; some authors ask not to distribute their work directly for download.
#
# Please be advised that all the download links collected here are >not< meant to be used
# for standalone download and distribution of the data files linked.

# It is your responsibility to check authors citation requirements and data usage restrictions
# if you want to use any of the files outside of their original purpose (i.e. incorporation to ActiveDriverDB)

# In effort to acknowledge all authors of the data used in ActiveDriverDB we prepared acknowledgments section on:
# https://activedriverdb.org/publications/


for required_program in 'wget' 'unzip' 'Rscript' 'tar' 'synapse'
do
  hash $required_program 2>/dev/null || {
    echo >&2 "$required_program is required but it is not installed. Aborting."
    exit 1
  }
done

wget https://gist.githubusercontent.com/krassowski/8c9710fa20ac944ec8d47ac4a0ac5b4a/raw/444fcc584bc10b5e504c05a6063a281cee808c9c/ucsc_download.sh
source ucsc_download.sh
# refseq mRNA summaries
get_whole_genome_table refseq_summary.tsv.gz genes refGene hgFixed.refSeqSummary gzip
# some of protein mappings (RefSeq)
get_whole_genome_table refseq_link.tsv.gz genes refGene hgFixed.refLink gzip
rm ucsc_download.sh

# full gene name
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

# hierarchy tree
wget ftp://ftp.ebi.ac.uk/pub/databases/interpro/ParentChildTreeFile.txt

# entry list (all data)
wget ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz

# protein mappings (external references)
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz

# uniprot sequences
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

# pathway list
wget http://biit.cs.ut.ee/gprofiler/gmt/gprofiler_hsapiens.NAME.gmt.zip
unzip gprofiler_hsapiens.NAME.gmt.zip
mv gprofiler_hsapiens.NAME.gmt/hsapiens.pathways.NAME.gmt .
rm gprofiler_hsapiens.NAME.gmt.zip
rm -r gprofiler_hsapiens.NAME.gmt
rm hsapiens.OMIM.NAME.gmt
rm hsapiens.MI.NAME.gmt
rm hsapiens.HPA.NAME.gmt
rm hsapiens.HP.NAME.gmt
rm hsapiens.GO.NAME.gmt
rm hsapiens.CORUM.NAME.gmt
rm hsapiens.BIOGRID.NAME.gmt
rm hsapiens.REAC.NAME.gmt
rm hsapiens.TF.NAME.gmt

#  All below are dropbox-dependent ===

mkdir -p drugbank
cd drugbank<commit_msg>Add splice isoforms from UniProt to download list<commit_after>#!/usr/bin/env bash
# Please be advised that files downloaded using this script are subject of different licencing policies
# and use of some files may be forbidden for commercial purposes. Authors of some files ask for citation
# if you use their work; some authors ask not to distribute their work directly for download.
#
# Please be advised that all the download links collected here are >not< meant to be used
# for standalone download and distribution of the data files linked.

# It is your responsibility to check authors citation requirements and data usage restrictions
# if you want to use any of the files outside of their original purpose (i.e. incorporation to ActiveDriverDB)

# In effort to acknowledge all authors of the data used in ActiveDriverDB we prepared acknowledgments section on:
# https://activedriverdb.org/publications/


for required_program in 'wget' 'unzip' 'Rscript' 'tar' 'synapse'
do
  hash $required_program 2>/dev/null || {
    echo >&2 "$required_program is required but it is not installed. Aborting."
    exit 1
  }
done

wget https://gist.githubusercontent.com/krassowski/8c9710fa20ac944ec8d47ac4a0ac5b4a/raw/444fcc584bc10b5e504c05a6063a281cee808c9c/ucsc_download.sh
source ucsc_download.sh
# refseq mRNA summaries
get_whole_genome_table refseq_summary.tsv.gz genes refGene hgFixed.refSeqSummary gzip
# some of protein mappings (RefSeq)
get_whole_genome_table refseq_link.tsv.gz genes refGene hgFixed.refLink gzip
rm ucsc_download.sh

# full gene name
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

# hierarchy tree
wget ftp://ftp.ebi.ac.uk/pub/databases/interpro/ParentChildTreeFile.txt

# entry list (all data)
wget ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz

# protein mappings (external references)
wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz

# uniprot sequences
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz

# pathway list
wget http://biit.cs.ut.ee/gprofiler/gmt/gprofiler_hsapiens.NAME.gmt.zip
unzip gprofiler_hsapiens.NAME.gmt.zip
mv gprofiler_hsapiens.NAME.gmt/hsapiens.pathways.NAME.gmt .
rm gprofiler_hsapiens.NAME.gmt.zip
rm -r gprofiler_hsapiens.NAME.gmt
rm hsapiens.OMIM.NAME.gmt
rm hsapiens.MI.NAME.gmt
rm hsapiens.HPA.NAME.gmt
rm hsapiens.HP.NAME.gmt
rm hsapiens.GO.NAME.gmt
rm hsapiens.CORUM.NAME.gmt
rm hsapiens.BIOGRID.NAME.gmt
rm hsapiens.REAC.NAME.gmt
rm hsapiens.TF.NAME.gmt

#  All below are dropbox-dependent ===

mkdir -p drugbank
cd drugbank
{'fraction_non_alphanumeric': 0.0842911877394636, 'fraction_numerical': 0.017879948914431672, 'mean_word_length': 4.958695652173913, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 9, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 15, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6056767', 'n_tokens_mistral': 2059, 'n_tokens_neox': 1913, 'n_words': 496}