linux--碱基序列处理

1. 从基因注释文件提取基因信息
   Zea_mays.B73_RefGen_v4.42.gtf gtf格式的注释文件

• 提取所有基因的位置信息

cat Zea_mays.B73_RefGen_v4.42.gtf|awk -F "\t" '{if($3~/gene/)print $1","$4","$5","$9}' >B73-V442.position.txt

• 提取制定染色体的所有基因的位置信息
  提取chr5
  cat Zea_mays.B73_RefGen_v4.42.gtf|awk -F "\t" '{if($3~/gene/&&$1~/5/)print $1","$4","$5","$9}' >B73-V442.Chr5.csv
• 提取chr3,chr5

cat Zea_mays.B73_RefGen_v4.42.gtf|awk -F "\t" '{if($3~/gene/&&$1~/^[3,5]/)print $1","$4","$5","$9}' 

• 提取指定染色体指定区间的所有基因
  指定第3条染色体，区间左侧是100450260，区间右侧是112424507的所有的基因和其位置信息

cat Zea_mays.B73_RefGen_v4.42.gtf|awk -F "\t" '{if($3~/gene/&&$1~/3/&&$4>100450260&&$5<112424507)print $1","$4","$5","$9}'

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