#!/bin/bash

# Scripts that take a feature CSV file and generate the corresponding
# hypergraphs relating them to geneNodes.  That is for each feature of
# name <GENE_NAME> produce:
#
# EquivalenceLink <1, 1>
#     PredicateNode <GENE_NAME>
#     LambdaLink
#         VariableNode $X
#         EvaluationLink
#             PredicateNode "overexpressed"
#             ListLink
#                 GeneNode <GENE_NAME>
#                 $X

set -u
# set -x

####################
# Source common.sh #
####################
PRG_PATH="$(readlink -f "$0")"
PRG_DIR="$(dirname "$PRG_PATH")"
. "$PRG_DIR/common.sh"

####################
# Program argument #
####################
if [[ $# == 0 || $# -gt 3 ]]; then
    echo "Usage: $0 FEATURE_CSV_FILE [-o OUTPUT_FILE]"
    echo "Example: $0 oldvscontrolFeatures.csv -o oldvscontrol-features-and-genes.scm"
    exit 1
fi

readonly FEATURE_CSV_FILE="$1"
shift
OUTPUT_FILE="/dev/stdout"
while getopts "o:" opt; do
    case $opt in
        o) OUTPUT_FILE="$OPTARG"
            ;;
    esac
done

########
# Main #
########

# Check that the header is correct (if not maybe the file format has
# changed)
header=$(head -n 1 "$FEATURE_CSV_FILE")
expected_header='"gene","Freq","level"'
if [[ "$header" != "$expected_header" ]]; then
    fatalError "Wrong header format: expect '$expected_header' but got '$header'"
fi

OLDIFS="$IFS"
IFS=","
while read feature freq level; do
    cat <<EOF
(EquivalenceLink
    (PredicateNode $feature)
    (LambdaLink
        (VariableNode "\$X")
        (EvaluationLink
            (PredicateNode "overexpressed")
            (ListLink
                (GeneNode $feature)
                (VariableNode "\$X"))))
EOF
done < <(tail -n +2 "$FEATURE_CSV_FILE") > "$OUTPUT_FILE"
IFS="$OLDIFS"