我的源文件:Test.txt
注意:文件是制表符分隔的,少数列没有列名:
Chr Start End Alt Value
Exo 0 10 . 1.50 . 20:-2 30:0.9 50:50 50
Exo 1 20 . 1.50 . 20:-1 30:-1 50:50 50
Exo 2 30 . 1.50 . 20:0.02 30:0.9 50:50 50
Exo 3 40 . 1.50 . 20:-1 30:-2 50:50 50
Nem 3 40 . 1.50 . 20:-1 30:-2 50:50 50
在上面的文件上尝试实现以下文件操作,例如:
1)第7列和第8列需要分割':'并且需要在更改后给出列名称,例如“mod1”,“mod2”,“mod3”,“mod4”。
2) 之后,将拆分的列移至“值”列旁边,并在“mod4”旁边再放置一个“注释”列(在该注释列中需要空白数据)。
3)过滤列“Mod2”所有大于0.01的值被删除
最终结果需要存储在输出文件夹中,例如:
Chr Start End Alt Value mod1 mod2 mod3 mod4 comment
Exo 0 10 -1 1.50 20 -2 30 0.9 -1 50:50 50
Exo 1 20 -1 1.50 20 -1 30 -1 -1 50:50 50
Exo 3 40 -1 1.50 20 -1 30 -2 -1 50:50 50
我尝试了以下操作并实现了一些操作,其中一些操作还剩下:
#!bin/bash
cd /home/uxm/Desktop/Shell/
# Replace the only dots (.) by -1
awk -F'\t' '{for(i=1;i<=NF;i++){sub(/^\.$/,"-1",$i)}} 1' OFS="\t" Test.txt | tail >> Test1.txt
# splitted 7th no column by delimitted ":"
awk '{ split($7, a, ":"); print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"a[1]"\t"a[2]"\t"$8"\t"$9"\t"$10"\t"$11 >> "testfile1.tmp"; }' Test1.txt;
mv testfile1.tmp Test2.txt;
# splitted 8th no column by delimitted ":"
awk '{ split($9, a, ":"); print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"a[1]"\t"a[2]"\t"$10"\t"$11 >> "testfile2.tmp"; }' Test2.txt;
mv testfile2.tmp Test3.txt;
# Give name to splitted columns
awk -F'\t' -v OFS="\t" 'NR==1{$11="nCol\tMod1\tMod2\tMod3\tMod4"}1' Test3.txt >> Test4.txt
# Filter data by "Exo" word
awk -F'\t' 'NR==1;{ if($1 == "Exo") { print }}' Test4.txt | tail >> Test5.txt
答案1
这是一个awk
执行您列举的步骤的脚本。在一个脚本中执行所有操作的好处是不必awk
多次运行并将中间结果存储在文件或变量中。
BEGIN { OFS = FS = "\t" }
NR == 1 {
# Add new column headers
# First four "mod" headers
for (i = 1; i <= 4; ++i)
$(NF + 1) = "mod" i
# Then a "comment" header
$(NF + 1) = "comment"
# Output and continue with next input line
print
next
}
# Ignore lines that don't have "Exo" in the first column
$1 != "Exo" { next }
{
# Working our way "backwards" from column 13 down to 1
# Shift the last two columns right by three steps
$13 = $10
$12 = $9
# Set column 11 to column 6, or to -1 if it's a dot
if ($6 == ".")
$11 = -1
else
$11 = $6
# Empty the comment column
$10 = ""
# Move column 8 into column 9
$9 = $8
# Split column 9 into columns 8 and 9
split($9, a, ":")
$9 = a[2]
$8 = a[1]
# Split column 7 into columns 6 and 7
split($7, a, ":")
$7 = a[2]
$6 = a[1]
# Column 5 remains unmodified
# Put -1 in column 4 if it's a dot
if ($4 == ".") $4 = -1
# Columns 1, 2, 3 remains unmodified
}
# Output if we want this line
$7 <= 0.01 { print }
运行它:
$ awk -f script.awk Test.txt
Chr Start End Alt Value mod1 mod2 mod3 mod4 comment
Exo 0 10 -1 1.50 20 -2 30 0.9 -1 50:50 50
Exo 1 20 -1 1.50 20 -1 30 -1 -1 50:50 50
Exo 3 40 -1 1.50 20 -1 30 -2 -1 50:50 50
我从您自己的代码中假设您只对这些Exo
行感兴趣,所以我让脚本只查看这些行。我假设 thaAlt
列(以及原始第一个无名列)中的任何点都应该更改为-1
,也可以通过查看您的代码来更改。