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rec3141/get-kos.sh

Created April 24, 2018 01:17
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extract specific HMMs from FOAM
Raw
get-kos.sh
#!/bin/bash
Search=$1
grep -i $Search FOAM-onto_rel1.tsv > $Search.ont
grep -i $Search FOAM-onto_rel1.tsv | cut -f5 > $Search.ko
wc -l $Search.ko
rm $Search.acc
grep -A1 -f $Search.ko ./../FOAM/FOAM-hmm_rel1a_switch.hmm | grep NAME | tr -s ' ' | cut -f2 -d' ' | sort -u > $Search.acc
wc -l $Search.acc
~/apps/hmmer/binaries/hmmfetch -f ./../FOAM/FOAM-hmm_rel1a_switch.hmm $Search.acc > $Search.hmm
wc -l $Search.hmm
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