mirror of
https://github.com/samsledje/D-SCRIPT.git
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56 lines
1.6 KiB
Bash
Executable File
56 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
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ORGS=( ecoli yeast worm mouse fly )
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TOPSY_TURVY=
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EMBEDDING_DIR=/afs/csail.mit.edu/u/s/samsl/Work/TT3D/FoldSeek_BriefCommunication/embeddings/
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SEQ_DIR=seqs-pairs/pairs
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FOLDSEEK_FASTA=../data/r3-ALLSPECIES_foldseekrep_seq.fa
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FOLDSEEK_VOCAB=../data/foldseek_vocab.json
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MODEL_PARAMS=""
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DEVICE=0
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usage() {
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echo "USAGE: ./test.sh [-d DEVICE] [-m MODEL] [-T MODEL_TYPE]
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OPTIONS:
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-d DEVICE: Device used
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-m MODEL: The model sav file
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-T: Set this flag if if the model passed by the '-m MODEL' command is a TT3D Model. Unset this for Topsy-Turvy/D-SCRIPT
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"
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}
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while getopts "d:m:T" args; do
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case $args in
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d) DEVICE=${OPTARG}
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;;
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m) MODEL=${OPTARG}
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;;
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T) MODEL_PARAMS="${MODEL_PARAMS} --add_foldseek_after_projection --foldseek_vocab ${FOLDSEEK_VOCAB} --foldseek_fasta ${FOLDSEEK_FASTA} --allow_foldseek"
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;;
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*) usage
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exit 1;
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esac
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done
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# Construct the folder
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OUTPUT_FLD=${MODEL%/*}
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OUTPUT_FILE=${MODEL##*/}
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OUTPUT_FILE_PREF=${OUTPUT_FILE%.*}
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OUTPUT_FOLDER=${OUTPUT_FLD}/eval-${OUTPUT_FILE_PREF}
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echo "Output folder: ${OUTPUT_FOLDER}, model: ${MODEL}, DEVICE: ${DEVICE}"
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if [ ! -d ${OUTPUT_FOLDER} ]; then mkdir $OUTPUT_FOLDER; fi
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for ORG in ${ORGS[@]}
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do
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EMBEDDING=${EMBEDDING_DIR}/${ORG}.h5
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TEST=${SEQ_DIR}/${ORG}_test.tsv
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OP_FOLDER_ORG=${OUTPUT_FOLDER}/${ORG}
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if [ ! -d ${OP_FOLDER_ORG} ]; then mkdir -p ${OP_FOLDER_ORG}; fi
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OP_FILE=${OP_FOLDER_ORG}/${OUTPUT_FILE}
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dscript evaluate --model ${MODEL} --embedding ${EMBEDDING} --test ${TEST} -d $DEVICE ${MODEL_PARAMS} -o $OP_FILE
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done
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