似乎并没有chromap的使用，我需要的是chromap和yahs联合进行HIC辅助染色体水平组装，需要用到这些参数，请整理参数进脚本“# chromap比对步骤
# 基于博客：https
://xuzhougeng.blog.youkuaiyun.com/article/details/
128769452
set -e
# 检查参数
if [ "$#" -ne 3 ]; then
echo "用法
: $0 <contigs.fa> <R
1.fastq> <R2.fastq>"
exit
1
fi
CONTIGS=$
1
R
1=$2
R2=$3
echo "=== 开始chromap比对 ==="
echo "Contigs
: $CONTIGS"
echo "R
1 reads
: $R
1"
echo "R2 reads
: $R2"
# 创建索引
echo "创建contigs索引..."
samtools faidx $CONTIGS
chromap -i -r $CONTIGS -o contigs.index
# 比对
echo "开始Hi-C数据比对..."
chromap \
--preset hic \
-r $CONTIGS \
-x contigs.index \
--remove-pcr-duplicates \
-
1 $R
1 \
-2 $R2 \
--SAM \
-o aligned.sam \
-t 8
# 转换为BAM并排序
echo "转换为BAM格式并排序..."
samtools view -bh aligned.sam | samtools sort -@ 8 -n > aligned.bam
rm aligned.sam
echo "比对完成！结果文件：aligned.bam"”#!/bin/bash
# yahs scaffolding步骤
# 基于博客：https
://xuzhougeng.blog.youkuaiyun.com/article/details/
128769452
set -e
# 检查参数
if [ "$#" -ne 2 ]; then
echo "用法
: $0 <contigs.fa> <aligned.bam>"
exit
1
fi
CONTIGS=$
1
BAM=$2
echo "=== 开始yahs scaffolding ==="
echo "Contigs
: $CONTIGS"
echo "BAM file
: $BAM"
# 转换BAM到BED格式
echo "转换BAM到BED格式..."
samtools view -bh -u -F0xF0C -q0 $BAM | \
bedtools bamtobed | \
awk -v OFS='\t' '{$4=substr($4,
1,length($4)-2); print}' > aligned.bed
# 运行yahs
echo "运行yahs scaffolding..."
yahs $CONTIGS aligned.bed
echo "Scaffolding完成！"
echo "主要结果文件："
echo "- yahs.out_scaffolds_final.agp"
echo "- yahs.out_scaffolds_final.fa"
echo "- yahs.out.bin"“#!/bin/bash
# 为JuiceBox准备输入文件
# 基于博客：https
://xuzhougeng.blog.youkuaiyun.com/article/details/
128769452
set -e
# 检查参数
if [ "$#" -ne 2 ]; then
echo "用法
: $0 <yahs_output_prefix> <contigs.fa>"
exit
1
fi
YAHS_PREFIX=$
1
CONTIGS=$2
echo "=== 为JuiceBox准备输入文件 ==="
echo "YAHS prefix
: $YAHS_PREFIX"
echo "Contigs
: $CONTIGS"
# 检查必需文件
if [ ! -f "${YAHS_PREFIX}.bin" ]; then
echo "错误：找不到 ${YAHS_PREFIX}.bin 文件"
exit
1
fi
if [ ! -f "${YAHS_PREFIX}_scaffolds_final.agp" ]; then
echo "错误：找不到 ${YAHS_PREFIX}_scaffolds_final.agp 文件"
exit
1
fi
# 准备juicer输入
echo "准备juicer pre输入..."
juicer pre -a -o out_
JBAT \
${YAHS_PREFIX}.bin \
${YAHS_PREFIX}_scaffolds_final.agp \
${CONTIGS}.fai
# 生成.hic文件
echo "生成.hic文件..."
JUICER="juicer_tools.jar"
if [ ! -f "$JUICER" ]; then
echo "错误：找不到 juicer_tools.jar，请先下载"
exit
1
fi
asm_size=$(awk '{s+=$2} END{print s}' ${CONTIGS}.fai)
java -Xmx8G -jar $JUICER \
pre out_
JBAT.txt out_
JBAT.hic <(echo "assembly ${asm_size}")
echo "JuiceBox输入文件准备完成！"
echo "主要文件："
echo "- out_
JBAT.hic (可导入JuiceBox)"
echo "- out_
JBAT.assembly"
echo "- out_
JBAT.txt"”#!/bin/bash
# JuiceBox后处理步骤
# 基于博客：https
://xuzhougeng.blog.youkuaiyun.com/article/details/
128769452
set -e
# 检查参数
if [ "$#" -ne 2 ]; then
echo "用法
: $0 <review.assembly> <contigs.fa>"
exit
1
fi
REVIEW_ASSEMBLY=$
1
CONTIGS=$2
echo "=== JuiceBox后处理 ==="
echo "Review assembly
: $REVIEW_ASSEMBLY"
echo "Contigs
: $CONTIGS"
# 检查必需文件
if [ ! -f "$REVIEW_ASSEMBLY" ]; then
echo "错误：找不到 $REVIEW_ASSEMBLY 文件"
exit
1
fi
if [ ! -f "out_
JBAT.liftover.agp" ]; then
echo "错误：找不到 out_
JBAT.liftover.agp 文件"
exit
1
fi
# 运行juicer post
echo "运行juicer post处理..."
JUICER="juicer_tools.jar"
java -Xmx8G -jar $JUICER \
post -o out_
JBAT \
$REVIEW_ASSEMBLY \
out_
JBAT.liftover.agp \
$CONTIGS
echo "后处理完成！"
echo "最终结果："
echo "- out_
JBAT.FINAL.agp"
echo "- out_
JBAT.FINAL.fa"“
本文介绍了Python中的jbat1接口，它以其简洁性和易用性为开发者提供高效编程体验。通过示例展示了如何使用jbat1接口读取和处理文件，并提及其在网络请求、数据库操作、图形界面等多个方面的应用，帮助开发者提高开发效率。
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