匹配并将字符串附加到标头

Question

我想将字符串附加到FASTA文件中的序列标题。

输入：

>uce-101_seqname
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

期望的输出：

>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

示例代码：

awk -F ">" '{if($2 ~ /^uce/){print $0 " |" substr($2,1,7)} else {print $0}}' <inputfile>

示例代码仅适用于7个字符（例如，uce-101）。我需要它才能工作更多且少于7个字符（例如，uce-1，uce-10，uce-1001）。

Answer 1

我认为shellter在上面的评论中已经敲定了头。这样，您的awk行可以缩减为：

awk -F '>' '$2~/^uce/ { x=$2; sub(/_.*/,"",x); print $0, "|" x; next }1' file

结果：

>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

---

但是，如果您更喜欢sed解决方案，可以尝试：

sed '/^>uce/s/>\([^_]*\).*/& |\1/' file

结果：

>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

说明：

/^>uce/      # This is an address that specifies which lines are to be
             # examined or modified. In this case, only lines beginning
             # the string 'uce' are to be addressed.

s/../../     # Perform a substitution using the '/' delimiter

>\([^_]*\).* # This is the pattern to be matched. The '>' character is a
             # literal '>'. Escaped parentheses are then used to capture
             # a character class that says any character not an
             # underscore any (zero or more) number of times. All this
             # is then followed by any character any number of times.

& |\1        # This is the replacement string. The '&' character is the
             # whole pattern that was found. This is followed by a
             # literal space and a literal pipe character. '\1' is then
             # our pattern that we kept using our escaped parentheses.

Answer 2

这应该做：

awk -F">|_" 'NF>2 {$0=$0" |"$2}1' file
>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

将字段分隔符设置为>或_
如果行包含两个以上的字段，请重新创建行
打印所有行。

如果你需要测试uce，那么应该这样做：

awk -F">|_" '$2~/^uce/ {$0=$0" |"$2}1' file