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63 lines
2.0 KiB
Bash
Executable File
63 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
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TOPSY_TURVY=
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TRAIN=seqs-pairs/pairs/human_train.tsv
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TEST=seqs-pairs/pairs/human_test.tsv
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EMBEDDING=/afs/csail.mit.edu/u/s/samsl/Work/DSCRIPT_Dev_and_Testing/FoldSeek_BriefCommunication/embeddings/human.h5
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OUTPUT_BASE=/afs/csail.mit.edu/u/s/samsl/Work/DSCRIPT_Dev_and_Testing/FoldSeek_BriefCommunication/results
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OUTPUT_FOLDER=${OUTPUT_BASE}/tt
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OUTPUT_PREFIX=results-
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FOLDSEEK_FASTA=../data/r3-ALLSPECIES_foldseekrep_seq.fa
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usage() {
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echo "Usage ./train.sh [-d DEVICE] [-v] [-f] [-F foldseek_fasta_file]
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-v: When set, returns a Topsy-Turvy model
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-f: When set, returns a TT3D model
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-F: Used only when -f is set. When -f is set, use this argument to pass in the foldseek 3di sequences in the fasta format
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"
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}
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while getopts "d:t:fF:T:e:E:vo:p:" args; do
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case $args in
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d) DEVICE=${OPTARG}
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;;
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t) TRAIN=${OPTARG}
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;;
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T) TEST=${OPTARG}
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;;
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e) EMBEDDING=${OPTARG}
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;;
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E) EMBEDDING_DIM="--input-dim ${OPTARG}"
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;;
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v) TOPSY_TURVY="--topsy-turvy --glider-weight 0.2 --glider-thres 0.925";
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;;
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o) OUTPUT_FOLDER=${OUTPUT_BASE}/${OPTARG}
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;;
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p) OUTPUT_PREFIX=${OPTARG}
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;;
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f) FOLDSEEK=1
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;;
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F) FOLDSEEK_FASTA=${OPTARG}
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;;
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*) usage
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exit 1;;
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esac
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done
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FOLDSEEK_CMD=""
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if [ ! -z $FOLDSEEK ]; then FOLDSEEK_CMD="--allow_foldseek --foldseek_fasta ${FOLDSEEK_FASTA} --add_foldseek_after_projection"; fi
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if [ ! -d ${OUTPUT_FOLDER} ]; then mkdir -p $OUTPUT_FOLDER; fi
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dscript train --train $TRAIN --test $TEST --embedding $EMBEDDING $TOPSY_TURVY \
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--outfile ${OUTPUT_FOLDER}/results.log \
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--save-prefix ${OUTPUT_FOLDER}/ep_ \
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--lr 0.0005 --lambda 0.05 --num-epoch 10 ${EMBEDDING_DIM}\
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--weight-decay 0 --batch-size 25 --pool-width 9 \
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--kernel-width 7 --dropout-p 0.2 --projection-dim 100 \
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--hidden-dim 50 --kernel-width 7 --device $DEVICE $FOLDSEEK_CMD
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