将字符串匹配并附加到 headers

Question

我想将字符串附加到 FASTA 文件中的序列 headers。

输入：

>uce-101_seqname
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

期望的输出：

>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

示例代码：

awk -F ">" '{if( ~ /^uce/){print [=13=] " |" substr(,1,7)} else {print [=13=]}}' <inputfile>

示例代码仅适用于 7 个字符（例如 uce-101）。我需要它适用于大于和小于 7 个字符（例如 uce-1、uce-10、uce-1001）。

Answer 1

我认为 shellter has hit the nail on the head with his comment above. With that, your line of awk 可以简化为：

awk -F '>' '~/^uce/ { x=; sub(/_.*/,"",x); print [=10=], "|" 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，您可以尝试：

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

结果：

>uce-101_seqname |uce-101
GGCTGGCACCAGTTAACTTGGGATATTGGAGTGAAAAGGCCCGTAATCAGCCTTCGGTCATGTAGAACAATGCATAAAATTAAATTGACATTAATGAATAATTGTGTAATGAAAATGGA

解释：

/^>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.

& |        # 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. '' is then
             # our pattern that we kept using our escaped parentheses.

Answer 2

应该这样做：

awk -F">|_" 'NF>2 {[=10=]=[=10=]" |"}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，重新创建行
打印所有行。

如果您需要测试 uce，那么应该这样做：

awk -F">|_" '~/^uce/ {[=11=]=[=11=]" |"}1' file

将字符串匹配并附加到 headers

matching and appending strings to headers

awk

sed

fasta

输入：

期望的输出：

示例代码：