使用grep和单词计数添加标头

Question

大家好，我有很多（200个左右）的文件

>Sample_NameA
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
>Sample_NameB
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT

我需要在包含样本数量的每个文件，字母数量（a，c，g，t）和第一。

因此，例如，第一个文件应该看起来像这样：

2 441 1
>Sample_NameA
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
>Sample_NameB
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT

我正在考虑使用第一个grep">"来计算样本的数量，因为每个示例名称都先于此，并使用wc来计算字符的数量直到另一个>，但我无法管理。片刻之后，我将在到目前为止的脚本上载我的脚本，但是如果有人解决了它，我会非常感谢它。

感谢ID Advance。

Answer 1

这个尴尬可以在一个命令中完成所有这些操作：

awk '{if (d) d=d RS $0; else d=$0}
      />/{s++;next}
      s==1 && /[ACGT]/{gsub(/[^ACGT]+/, ""); n+=length($0)}
      END{print s, n, "1" RS d}' file
2 441 1
>Sample_NameA
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
>Sample_NameB
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT
ACGTGTCTAGTATGCATGCATAGCTACGACTACGACTAGCATCAGCATCGACTAGCATCGACT

Answer 2

#!/bin/bash
DATA="$1" # for readability; give /path/to/data/file as first argument to the script
SAMPLES=$(grep -c '>' "$DATA")
CHARS=$(grep -v '>' "$DATA" | wc -c)
echo "$SAMPLES $CHARS 1"
cat "$DATA"

Answer 3

无法想到只用一个GREP来完成此操作的方法，但肯定可以使用一些管道可行。

，例如

> grep -E "^>" file 
2
> grep -E -v "^>" file | grep -o "[ACGT]" | wc -l
756

Answer 4

，并完全归功于@anubhava，这是一种无法将整个文件保留在内存中的方法：

ed file <<END
1i
$(awk '/^>/ {s++; next} s==1 {l+=length()} END {print s,l,1}' file)
.
w
q
END