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add script for filtering phosphosite dataset
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kamurani committed Jul 19, 2022
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17 changes: 17 additions & 0 deletions scripts/phosphosite_dump_filtering.sh
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#! /usr/bin/env bash
# Get list of all kinase types for H. Sapiens
cat ../datasets/phosphoELM_all_2015-04.dump |\
grep -i "homo sapiens" |\
cut -f1,6,8 | cut -f2 | sed 's/^$/UNKNOWN/' | sort | uniq

# Get all phosphosites with known kinase in humans
cat ../datasets/phosphoELM_all_2015-04.dump |\
grep -i "homo sapiens" |\
cut -f1,6,8 | grep -i "\S\sHomo sapiens" |\
#cut -f2 | sort | uniq | wc -l


# WITH USEFUL FIELDS
cat ../datasets/phosphoELM_all_2015-04.dump |\
grep -i "homo sapiens" |\
cut -f1,3,4,6,8 | grep -i "\S\sHomo sapiens" > human_known_kin

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