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@@ -59,6 +59,16 @@ with open("sample_sheet.csv", 'w') as f:
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##########################################################
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# rule all: 最终想要生成的文件
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##########################################################
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+def get_motifs_from_meme(meme_file):
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+ motifs = []
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+ with open(meme_file, 'r') as file:
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+ for line in file:
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+ if line.startswith("MOTIF"):
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+ parts = line.split()
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+ motif_name = parts[2] + "_" + parts[1] # 第二列和第三列的组合
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+ motifs.append(motif_name)
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+ return motifs
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+
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rule all:
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input:
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#####################################
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@@ -105,6 +115,11 @@ rule all:
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"quality_control/estimate_read_filtering.tsv",
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# cross correlation 质控表格
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"quality_control/cross_correlation_summary.tsv" if config["cross_correlation"]["do"] else [],
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+ #####################################
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+ # 足迹分析
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+ #####################################
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+ "footprinting/bindetect_results.txt",
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+ expand("footprinting/{motif}/{motif}_Plot{plot}.pdf", motif=get_motifs_from_meme("motif_databases/JASPAR/JASPAR2022_CORE_plants_non-redundant_v2.meme"), plot=["Aggregate", "Heatmap"])
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##########################################################
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# 使用fastp进行原始数据质控和过滤，自动判断 SE？PE？
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@@ -366,7 +381,7 @@ rule callpeak_with_macs3:
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threads: 1
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params:
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control=lambda wildcards: f"-c clean_bams/{config['samples'][wildcards.replicate]}_final.bam" if config['samples'][wildcards.replicate] else "",
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- format="BAMPE" if SEQ_TYPE == 'PE' else "BAM",
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+ format="BAMPE" if SEQ_TYPE == 'PE' and '--nomodel' not in config["macs3"]["extra"] else "BAM",
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gsize=config["gsize"],
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PEAK_TYPE="--broad" if PEAK_TYPE == "broad" else "",
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extra = config["macs3"]["extra"] if config["macs3"]["extra"] else ""
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@@ -672,6 +687,89 @@ rule combine_fastp_reports:
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Rscript {params.peaksnake_home}/scripts/combine_fastp_report.R --input {input} --output quality_control/ 1>{log} 2>&1
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"""
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+##########################################################
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+# 使用 TOBIAS 进行足迹分析
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+##########################################################
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+rule merge_replicate_bams:
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+ input:
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+ bams=lambda wildcards: expand("clean_bams/{sample}_{rep}_final.bam", sample = wildcards.sample, rep=SAMPLE_TO_REPLICATE[wildcards.sample])
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+ output:
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+ bam="clean_bams/{sample}_merged.bam"
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+ shell:
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+ """
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+ samtools merge -o {output.bam} {input.bams}
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+ samtools index {output.bam}
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+ """
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+
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+rule ATACorrect:
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+ input:
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+ bam="clean_bams/{sample}_merged.bam",
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+ genome=config["genome"],
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+ merged_peaks_bed="clean_peaks/merge/merged_peaks.bed"
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+ output:
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+ bw="footprinting/{sample}_corrected.bw"
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+ params:
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+ prefix="{sample}"
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+ threads: 8
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+ log: "logs/{sample}_ATACorrect.log"
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+ singularity:
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+ PEAKSNAKE_HOME + "/sifs/tobias_20231231.sif"
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+ shell:
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+ """
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+ TOBIAS ATACorrect --window 10 --bam {input.bam} --genome {input.genome} --peaks {input.merged_peaks_bed} --outdir footprinting --prefix {params.prefix} --cores {threads} 1>{log} 2>&1
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+ """
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+
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+rule FootprintScores:
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+ input:
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+ bw="footprinting/{sample}_corrected.bw",
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+ merged_peaks_bed="clean_peaks/merge/merged_peaks.bed"
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+ output:
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+ bw="footprinting/{sample}_footprints.bw"
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+ params:
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+ prefix={sample}
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+ threads: 8
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+ log: "logs/{sample}_FootprintScores.log"
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+ singularity:
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+ PEAKSNAKE_HOME + "/sifs/tobias_20231231.sif"
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+ shell:
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+ """
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+ TOBIAS FootprintScores --window 10 --signal {input.bw} --regions {input.merged_peaks_bed} --output {output.bw} --cores {threads} 1>{log} 2>&1
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+ """
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+
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+rule BINDetect:
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+ input:
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+ bws=expand("footprinting/{sample}_footprints.bw", sample=SAMPLE_TO_REPLICATE.keys()),
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+ merged_peaks_bed="clean_peaks/merge/merged_peaks.bed",
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+ genome=config["genome"]
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+ output:
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+ "footprinting/bindetect_results.txt"
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+ params:
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+ samples=" ".join(SAMPLE_TO_REPLICATE.keys())
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+ threads: 8
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+ log: "logs/BINDetect.log"
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+ singularity:
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+ PEAKSNAKE_HOME + "/sifs/tobias_20231231.sif"
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+ shell:
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+ """
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+ TOBIAS BINDetect --motifs motif_databases/JASPAR/JASPAR2022_CORE_plants_non-redundant_v2.meme --signals {input.bws} --genome {input.genome} --peaks {input.merged_peaks_bed} --outdir footprinting --cond_names {params.samples} --cores {threads}
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+ """
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+
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+rule plot_per_motif:
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+ input:
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+ motif_bed="footprinting/{motif}/beds/{motif}_all.bed",
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+ bws=expand("footprinting/{sample}_corrected.bw", sample=SAMPLE_TO_REPLICATE.keys())
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+ output:
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+ aggregate_pdf="footprinting/{motif}/{motif}_PlotAggregate.pdf",
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+ heatmap_pdf="footprinting/{motif}/{motif}_PlotHeatmap.pdf"
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+ threads: 1
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+ singularity:
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+ PEAKSNAKE_HOME + "/sifs/tobias_20231231.sif"
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+ shell:
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+ """
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+ TOBIAS PlotAggregate --TFBS {input.motif_bed} --signals {input.bws} --output {output.aggregate_pdf} --share_y both --plot_boundaries --signal-on-x
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+ TOBIAS PlotHeatmap --TFBS {input.motif_bed} --signals {input.bws} --output {output.heatmap_pdf} --sort_by -2
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+ """
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+
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##########################################################
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# cross correlation
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##########################################################
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