Created
April 24, 2018 01:17
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extract specific HMMs from FOAM
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| #!/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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