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王子叶
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add bin for bioconda
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‎COMEBin/comebin_version.py‎

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__version__ = '1.0.1'
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__version__ = '1.0.2'

‎COMEBin/run_comebin.sh‎

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# Author of pipeline: Ziye Wang.
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# For questions, bugs, and suggestions, contact me at zwang17@fudan.edu.cn
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##############################################################################################################################################################
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VERSION="1.0.2"
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help_message () {
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echo ""
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echo "COMEBin version: $VERSION"
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echo "Usage: bash run_comebin.sh [options] -a contig_file -o output_dir -p bam_file_path"
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echo "Options:"
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echo ""
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echo " -b INT batch size for training process (default=1024)"
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echo "";}
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########################################################################################################
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######################## LOADING IN THE PARAMETERS AND RUNNING ########################
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########################################################################################################
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num_threads=5
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n_views=6
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#temperature=0.15

‎bin/run_comebin.sh‎

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#!/usr/bin/env bash
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##############################################################################################################################################################
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# This script is meant to be run COMEBin after obtaining the bam files.
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# Author of pipeline: Ziye Wang.
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# For questions, bugs, and suggestions, contact me at zwang17@fudan.edu.cn
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##############################################################################################################################################################
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VERSION="1.0.2"
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help_message () {
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echo ""
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echo "COMEBin version: $VERSION"
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echo "Usage: bash run_comebin.sh [options] -a contig_file -o output_dir -p bam_file_path"
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echo "Options:"
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echo ""
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echo " -a STR metagenomic assembly file"
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echo " -o STR output directory"
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echo " -p STR path to access to the bam files"
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echo " -n INT number of views for contrastive multiple-view learning (default=6)"
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echo " -t INT number of threads (default=5)"
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echo " -l FLOAT temperature in loss function (default=0.07 for assemblies with an N50 > 10000, default=0.15 for others)"
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echo " -e INT embedding size for comebin network (default=2048)"
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echo " -c INT embedding size for coverage network (default=2048)"
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echo " -b INT batch size for training process (default=1024)"
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echo "";}
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run_file_path=$(dirname $(which run_comebin.sh))
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if [[ $? -ne 0 ]]; then
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echo "cannot find run_comebin.sh file - something went wrong with the installation!"
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exit 1
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fi
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########################################################################################################
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######################## LOADING IN THE PARAMETERS AND RUNNING ########################
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########################################################################################################
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num_threads=5
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n_views=6
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#temperature=0.15
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emb_szs_forcov=2048
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emb_szs=2048
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batch_size=1024
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while getopts a:o:p:n:t:l:e:c:b: OPT; do
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case ${OPT} in
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a) contig_file=$(realpath ${OPTARG})
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;;
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o) output_dir=$(realpath ${OPTARG})
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;;
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p) bam_file_path=$(realpath ${OPTARG})
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;;
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n) n_views=${OPTARG}
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;;
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t) num_threads=${OPTARG}
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;;
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l) temperature=${OPTARG}
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;;
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e) emb_szs=${OPTARG}
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;;
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c) emb_szs_forcov=${OPTARG}
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;;
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b) batch_size=${OPTARG}
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;;
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\?)
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# printf "[Usage] `date '+%F %T'` -i <INPUT_FILE> -o <OUTPUT_DIR> -o <P
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#RODUCT_CODE> -s <SOFTWARE_VERSION> -t <TYPE>\n" >&2
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exit 1
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esac
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done
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cd ${run_file_path}/COMEBin
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# check parameter
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if [ -z "${contig_file}" -o -z "${output_dir}" -o -z "${bam_file_path}" ]; then
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help_message
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exit 1
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fi
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if [ -z "$temperature" ]; then
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# Compute the length of each sequence and sort using the awk command
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awk '/^>/ {if (seqlen) print seqlen; seqlen=0; next} {seqlen+=length($0)} END {print seqlen}' "$contig_file" | sort -rn > ${contig_file}_lengths.txt
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# CAL N50
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total_length=$(awk '{sum+=$1} END {print sum}' ${contig_file}_lengths.txt)
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target_length=$(awk -v total="$total_length" 'BEGIN {cutoff=total/2; current=0} {current+=$1; if (current >= cutoff) {print $1; exit}}' ${contig_file}_lengths.txt)
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# N50
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echo "N50: $target_length"
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# Check if N50 is greater than 10000 and set tau accordingly
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if [ "$target_length" -gt 10000 ]; then
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temperature=0.07
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else
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temperature=0.15
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fi
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echo "Tau(temperature): ${temperature}"
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else
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echo "Tau(temperature): ${temperature}"
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fi
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########################################################################################################
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###### Get augmentation data
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########################################################################################################
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folder=${output_dir}/data_augmentation
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keyword="_datacoverage_mean"
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if [ -d "$folder" ]; then
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echo "${output_dir}/data_augmentation exists."
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count=$(find "$folder" -maxdepth 1 -type f -name "*$keyword*" | wc -l)
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echo "Number of files containing '$keyword' in the folder: $count"
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if [ "$count" -ne ${n_views} ]; then
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echo "Running data augmentation."
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python main.py generate_aug_data --contig_file ${contig_file} \
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--out_augdata_path ${output_dir}/data_augmentation \
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--n_views ${n_views} --bam_file_path ${bam_file_path} --num_threads ${num_threads}
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else
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echo "No need to run data augmentation."
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fi
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else
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echo "${output_dir}/data_augmentation does not exist."
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echo "Running data augmentation."
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python main.py generate_aug_data --contig_file ${contig_file} \
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--out_augdata_path ${output_dir}/data_augmentation \
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--n_views ${n_views} --bam_file_path ${bam_file_path} --num_threads ${num_threads}
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fi
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if [[ $? -ne 0 ]] ; then echo "Something went wrong with running generating augmentation data. Exiting.";exit 1; fi
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########################################################################################################
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###### Get representation (training process)
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########################################################################################################
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folder=${output_dir}/comebin_res
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keyword="embeddings.tsv"
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if [ -d "$folder" ]; then
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echo "${output_dir}/comebin_res exists."
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count=$(find "$folder" -maxdepth 1 -type f -name "*$keyword*" | wc -l)
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echo "Number of files containing '$keyword' in the folder: $count"
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if [ "$count" -ne 2 ]; then
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echo "Running getting representation."
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python main.py train --data ${output_dir}/data_augmentation \
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--temperature ${temperature} --emb_szs_forcov ${emb_szs_forcov} \
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--batch_size ${batch_size} --emb_szs ${emb_szs} --n_views ${n_views} \
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--add_model_for_coverage \
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--output_path ${output_dir}/comebin_res --earlystop --addvars --vars_sqrt
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else
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echo "No need to run getting representation."
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fi
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else
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echo "${output_dir}/comebin_res does not exist."
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echo "Running getting representation."
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python main.py train --data ${output_dir}/data_augmentation \
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--temperature ${temperature} --emb_szs_forcov ${emb_szs_forcov} \
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--batch_size ${batch_size} --emb_szs ${emb_szs} --n_views ${n_views} \
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--add_model_for_coverage \
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--output_path ${output_dir}/comebin_res --earlystop --addvars --vars_sqrt
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fi
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if [[ $? -ne 0 ]] ; then echo "Something went wrong with running training network. Exiting.";exit 1; fi
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########################################################################################################
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#### Clustering (run Leiden-based clustering methods and get the final result)
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########################################################################################################
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emb_file=${output_dir}/comebin_res/embeddings.tsv
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seed_file=${contig_file}.bacar_marker.2quarter_lencutoff_1001.seed
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python main.py bin --contig_file ${contig_file} \
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--emb_file ${emb_file} \
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--output_path ${output_dir}/comebin_res \
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--seed_file ${seed_file} --num_threads ${num_threads}
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python main.py get_result --contig_file ${contig_file} \
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--output_path ${output_dir}/comebin_res \
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--seed_file ${seed_file} --num_threads ${num_threads}
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if [[ $? -ne 0 ]] ; then echo "Something went wrong with running clustering. Exiting.";exit 1; fi
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