62 lines
3.4 KiB
Bash
62 lines
3.4 KiB
Bash
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#!/bin/bash
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source /storage/data1/marmi/miniconda/installation/etc/profile.d/conda.sh
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conda activate marmi_methylome
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#перед каждым запуском заполнять эти три переменных и path_to_sample
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path_to_assembly="/storage/data1/marmi/dec_custom_libs_zvl/unicycler_assembly_custom"
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goal_dir="custom_libs_E_Coli_Zvl"
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path_to_tables="/storage/data1/marmi/dec_custom_libs_zvl/info_tables_repaired"
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mkdir /storage/data1/marmi/dec_custom_libs_zvl
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path_to_python="/storage/data1/marmi/trial_scripts/info_pol_mapq_union.py"
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mkdir ${path_to_tables}
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touch ${path_to_tables}/names_of_custom_chromosome.txt
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touch ${path_to_tables}/names_of_custom_plasmid.txt
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cat reads_fastp.txt | while read i || [[ -n $i ]];
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do
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dir=`echo $i| awk '{split($0, array); print array[1]}'`
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if [ "$dir" == "$goal_dir" ]; then
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sample=`echo $i| awk '{split($0, array); print array[4]}'`
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path_to_sample="/storage/data1/marmi/dec_custom_libs_repaired_${sample}"
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name_of_dir="union_${sample}"
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mkdir ${path_to_sample}/${name_of_dir}
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cd ${path_to_sample}/${name_of_dir}
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bwa mem -t 7 ${path_to_assembly}/assembly.fasta ../qc_source_files/custom_${sample}_1.fastq.gz \
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../qc_source_files/custom_${sample}_2.fastq.gz >custom_${sample}_paired.sam \
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2>bwa_mem_custom_${sample}_paired.log
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bwa mem -t 7 ${path_to_assembly}/assembly.fasta ../qc_source_files/custom_${sample}_u.fastq.gz \
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>custom_${sample}_unpaired.sam \
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2>bwa_mem_custom_${sample}_unpaired.log
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samtools view -Sb -o custom_${sample}_paired.bam custom_${sample}_paired.sam
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samtools view -Sb -o custom_${sample}_unpaired.bam custom_${sample}_unpaired.sam
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rm custom_${sample}_paired.sam
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rm custom_${sample}_unpaired.sam
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samtools sort -o custom_${sample}_paired_sorted.bam custom_${sample}_paired.bam
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samtools sort -o custom_${sample}_unpaired_sorted.bam custom_${sample}_unpaired.bam
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samtools merge -o custom_${sample}.bam \
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custom_${sample}_paired_sorted.bam custom_${sample}_unpaired_sorted.bam
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samtools index custom_${sample}.bam
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rm custom_${sample}_paired_sorted.bam
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rm custom_${sample}_unpaired_sorted.bam
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rm custom_${sample}_paired.bam
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rm custom_${sample}_unpaired.bam
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touch custom_${sample}_genome.txt
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touch custom_${sample}_plasmid.txt
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cat ${path_to_assembly}/chromosome_genome.txt | while read j || [[ -n $j ]];
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do
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samtools view -F 4 custom_${sample}.bam $j | grep 'MD:Z' >> custom_${sample}_genome.txt
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done
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cat ${path_to_assembly}/chromosome_plasmid.txt | while read j || [[ -n $j ]];
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do
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samtools view -F 4 custom_${sample}.bam $j | grep 'MD:Z' >> custom_${sample}_plasmid.txt
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done
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python3 ${path_to_python} ${sample}_genome ${path_to_sample}/${name_of_dir}/ ${path_to_tables}/
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python3 ${path_to_python} ${sample}_plasmid ${path_to_sample}/${name_of_dir}/ ${path_to_tables}/
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echo "custom_${sample}_genome_mapq20_table.txt" >>${path_to_tables}/names_of_custom_chromosome.txt
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echo "custom_${sample}_plasmid_mapq20_table.txt" >>${path_to_tables}/names_of_custom_plasmid.txt
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fi
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done
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conda deactivate
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conda activate marmi_telegram
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telegram-send "Work_custom_union_align second step ends at `date`."
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conda deactivate
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