1

大家好，我有很多（200 个左右）文件看起来像这样

>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、字母数量（A、C、G、T）和数字一的每个文件上添加一个标题。

因此，例如，第一个文件应如下所示：

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 ">" 来计算样本数，因为每个样本名称都在前面，并使用 wc 来计算字符数，直到另一个 >，但我无法管理它。稍后我将上传我的脚本和我目前所拥有的，但如果有人解决了它，我会非常感激它。

提前谢谢身份证。

4

4 回答 4

2

这个 awk 可以在一个命令中完成所有这些：

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
于 2014-02-05T18:49:02.613 回答
0

完全归功于@anubhava，这是一种不会将整个文件保存在内存中的方法：

ed file <<END
1i
$(awk '/^>/ {s++; next} s==1 {l+=length()} END {print s,l,1}' file)
.
w
q
END
于 2014-02-05T19:38:52.077 回答
0

就能做到这一点的方法，但用几个管道肯定是可行的。

例如

> grep -E "^>" file 
2
> grep -E -v "^>" file | grep -o "[ACGT]" | wc -l
756
于 2014-02-05T18:56:55.200 回答
0 
#!/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"
于 2014-02-05T18:49:15.097 回答