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Enhance run_comebin.sh and gen_cov_file.sh #34

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Enhance run_comebin.sh and gen_cov_file.sh #34

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44 changes: 36 additions & 8 deletions COMEBin/run_comebin.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,12 @@ VERSION="1.0.4"
help_message () {
echo ""
echo "COMEBin version: $VERSION"
echo "Usage: bash run_comebin.sh [options] -a contig_file -o output_dir -p bam_file_path"
echo "Usage: bash run_comebin.sh [options] -a contig_file -o output_dir -p bam_file_or_path"
echo "Options:"
echo ""
echo " -a STR metagenomic assembly file"
echo " -a STR metagenomic assembly file (supports .gz compressed files)"
echo " -o STR output directory"
echo " -p STR path to access to the bam files"
echo " -p STR path to a BAM file or directory containing BAM files"
echo " -n INT number of views for contrastive multiple-view learning (default=6)"
echo " -t INT number of threads (default=5)"
echo " -l FLOAT temperature in loss function (default=0.07 for assemblies with an N50 > 10000, default=0.15 for others)"
Expand All @@ -42,7 +42,7 @@ while getopts a:o:p:n:t:l:e:c:b: OPT; do
;;
o) output_dir=$(realpath ${OPTARG})
;;
p) bam_file_path=$(realpath ${OPTARG})
p) bam_path=$(realpath ${OPTARG})
;;
n) n_views=${OPTARG}
;;
Expand All @@ -64,22 +64,51 @@ while getopts a:o:p:n:t:l:e:c:b: OPT; do
done

# check parameter
if [ -z "${contig_file}" -o -z "${output_dir}" -o -z "${bam_file_path}" ]; then
if [ -z "${contig_file}" -o -z "${output_dir}" -o -z "${bam_path}" ]; then
help_message
exit 1
fi

# Create temporary directory for any temp files
temp_dir=$(mktemp -d -p /tmp comebin_XXXXXX)
cleanup() {
echo "Cleaning up temporary files..."
[ -d "$temp_dir" ] && rm -rf "$temp_dir"
[ -n "$temp_contig_file" -a -f "$temp_contig_file" ] && rm -f "$temp_contig_file"
[ -n "$temp_bam_dir" -a -d "$temp_bam_dir" ] && rm -rf "$temp_bam_dir"
}
trap cleanup EXIT

# Handle compressed assembly files
if [[ "$contig_file" =~ \.(gz|gzip)$ ]]; then
echo "Detected compressed assembly file. Decompressing to temporary location..."
temp_contig_file="${temp_dir}/$(basename "${contig_file%.*}")"
gunzip -c "$contig_file" > "$temp_contig_file"
contig_file="$temp_contig_file"
echo "Using decompressed file: $contig_file"
fi

sequence_count=$(grep -c "^>" "${contig_file}")
# Handle BAM file or directory
if [ -f "$bam_path" ] && [[ "$bam_path" =~ \.bam$ ]]; then
echo "Using single BAM file: $bam_path"
temp_bam_dir="${temp_dir}/bam_files"
mkdir -p "$temp_bam_dir"
ln -sf "$bam_path" "$temp_bam_dir/$(basename "$bam_path")"
bam_file_path="$temp_bam_dir"
echo "Created temporary BAM directory: $bam_file_path"
else
echo "Using BAM files from directory: $bam_path"
bam_file_path="$bam_path"
fi

sequence_count=$(grep -c "^>" "${contig_file}")

if (( sequence_count < ${batch_size} )); then
batch_size=${sequence_count}
fi

echo "Batch size: ${batch_size}"


if [ -z "$temperature" ]; then
# Compute the length of each sequence and sort using the awk command
awk '/^>/ {if (seqlen) print seqlen; seqlen=0; next} {seqlen+=length($0)} END {print seqlen}' "$contig_file" | sort -rn > ${contig_file}_lengths.txt
Expand Down Expand Up @@ -182,4 +211,3 @@ python main.py get_result --contig_file ${contig_file} \
--seed_file ${seed_file} --num_threads ${num_threads}

if [[ $? -ne 0 ]] ; then echo "Something went wrong with running clustering. Exiting.";exit 1; fi

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