使用特定符号之间匹配的 ID 字符串过滤多 fasta 文件

Question

我在这个问题上卡住了一段时间，尽管我发现了一组不同的类似问题 none 完全符合我的问题或解决了问题。所以这是交易：

我有一个 input.fasta ，格式如下：

>sp|O42363|APOA1_DANRE Apolipoprotein A-I OS=Danio rerio OX=7955 GN=apoa1 PE=2 SV=1
MKFVALALTLLLALGSQANLFQADAPTQLEHYKAAALVYLNQVKDQAEKALDNLDGTDYEQYKLQLSESLTKLQEYAQTTSQALTPYAETISTQLMENTKQLRERVMTDVEDLRSKLEPHRAELYTALQKHIDEYREKLEPVFQEYSALNRQNAEQLRAKLEPLMDDIRKAFESNIEETKSKVVPMVEAVRTKLTERLEDLRTMAAPYAEEYKEQLVKAVEEAREKIAPHTQDLQTRMEPYMENVRTTFAQMYETIAKAIQA
>sp|Q90260|ASL1B_DANRE Achaete-scute homolog 1b OS=Danio rerio OX=7955 GN=ascl1b PE=2 SV=1
MEATVVATTQLTQDSFYQPFSESLEKQDRECKVLKRQRSSSPELLRCKRRLTFNGLGYTIPQQQPMAVARRNERERNRVKQVNMGFQTLRQHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVSAVLQCGVPSPSVSNAYSAGPESPHSAYSSDEGSYEHLSSEEQELLDFTTWFDRYESGASMATKDWC
>sp|Q6TH01|C10_DANRE Protein C10 OS=Danio rerio OX=7955 GN=si:dkey-29f10.1 PE=2 SV=1
MASAPAQQPTLTVEQARVVLSEVIQAFSVPENAARMEEARESACNDMGKMLQLVLPVATQIQQEVIKAYGFNNEGEGVLKFARLVKMYETQDPEIAAMSVKLKSLLLPPLSTPPIGSGIPTS
>sp|Q6PFL6|CCD43_DANRE Coiled-coil domain-containing protein 43 OS=Danio rerio OX=7955 GN=ccdc43 PE=2 SV=1
MAAPEQIAGEFENWLNERLDSLEVDREVYGAYILGVLQEEESDEEQKDALQGILSAFLEEETLEEVCQEILKQWTECCSRSGAKSNQADAEVQAIASLIEKQAQIVVKQKEVSEDAKKRKEAVLAQYANVTDDEDEAEEEEQVPVGIPSDKSLFKNTNVEDVLNRRKLQRDQAKEDAQKKKEQDKMQREKDKLSKQERKDKEKKRTQKGERKR
>sp|P0C7U5|C5AR1_DANRE C5a anaphylatoxin chemotactic receptor 1 OS=Danio rerio OX=7955 GN=c5ar1 PE=3 SV=1
MDDNNSDWTSYDFGNDTIPSPNEISLSHIGTRHWITLVCYGIVFLLGVPGNALVVWVTGFRMPNSVNAQWFLNLAIADLLCCLSLPILMVPLAQDQHWPFGALACKLFSGIFYMMMYCSVLLLVVISLDRFLLVTKPVWCQNNRQPRQARILCFIIWILGLLGSSPYFAHMEIQHHSETKTVCTGSYSSLGHAWAITIIRSFLFFLLPFLIICISHWKVYHMTSSGRRQRDKSSRTLRVILALVLGFFLCWTPLH

和一个 ids.txt 列表，格式如下：

Q90260
Q6PFL6

我想提取所有带有 header 的 fasta 序列，其中 ids.txt 的 ID 是 header 的元素。我试过 grep -w -A 2 -Ff id_list.txt input.fasta --no-group-separator > out.fasta 但没用。

理想情况下，我想通过正则表达式检查以 >sp 开头的每一行的两个 | 之间的字符串是否与我的 idx.txt 中的任何 ID 匹配。如果是这样，将 header 和 fasta 存储在 out.fasta.

所以 out.fasta 看起来像这样：

>sp|Q90260|ASL1B_DANRE Achaete-scute homolog 1b OS=Danio rerio OX=7955 GN=ascl1b PE=2 SV=1
MEATVVATTQLTQDSFYQPFSESLEKQDRECKVLKRQRSSSPELLRCKRRLTFNGLGYTIPQQQPMAVARRNERERNRVKQVNMGFQTLRQHVPNGAANKKMSKVETLRSAVEYIRALQQLLDEHDAVSAVLQCGVPSPSVSNAYSAGPESPHSAYSSDEGSYEHLSSEEQELLDFTTWFDRYESGASMATKDWC
>sp|Q6PFL6|CCD43_DANRE Coiled-coil domain-containing protein 43 OS=Danio rerio OX=7955 GN=ccdc43 PE=2 SV=1
MAAPEQIAGEFENWLNERLDSLEVDREVYGAYILGVLQEEESDEEQKDALQGILSAFLEEETLEEVCQEILKQWTECCSRSGAKSNQADAEVQAIASLIEKQAQIVVKQKEVSEDAKKRKEAVLAQYANVTDDEDEAEEEEQVPVGIPSDKSLFKNTNVEDVLNRRKLQRDQAKEDAQKKKEQDKMQREKDKLSKQERKDKEKKRTQKGERKR

我很确定这可以通过 awk 或 grep 来表达，但我是 bash 的新手，所以我现在很难过。

提前致谢！ :)

Answer 1

使用 join 和 sort:

join -t \| -2 2 -o 2.1,2.2,2.3 <(sort ids.txt) <(sort -t \| -k2 input.fasta)

假设 input.fasta 中没有额外的 | 字符并且输出行的顺序不重要。

Answer 2

与awk:

awk -F'[|]' 'NR==FNR{ids[[=10=]];next} in ids' ids.txt input.fasta

解释：

我将文件 ids.txt 和 input.fasta 作为输入文件传递给 awk。顺序很重要。 -F'[|]' 将输入字段分隔符设置为 |.

脚本：

# NR  is the overall record (line) number
# FNR is the record (line) number in the current input file

NR==FNR {   # True as long as we are reading the first input file
    ids[[=11=]]   # Create a key in ids for every id from ids.txt
    next      # Don't process further actions
}

# Because of the 'next' statement above, we'll reach this point only
# when reading the second input file (input.fasta)
 in ids   # Print the current line if the second field
            # was found in the ids lookup

输出：

>sp|Q90260|ASL1B_DANRE Achaete-scute homolog 1b OS=Danio rerio OX=7955 GN=ascl1b PE=2 SV=1
>sp|Q6PFL6|CCD43_DANRE Coiled-coil domain-containing protein 43 OS=Danio rerio OX=7955 GN=ccdc43 PE=2 SV=1

更新：原来你还想打印匹配项下方的内容。这可以这样实现：

BEGIN {
    FS="[|]"
}

# NR  is the overall record (line) number
# FNR is the record (line) number in the current input file

NR==FNR {   # True as long as we are reading the first input file
    ids[[=13=]]   # Create a key in ids for every id from ids.txt
    next      # Don't process further actions
}

# Because of the 'next' statement above, we'll reach this point only
# when reading the second input file (input.fasta)
 in ids  {
    # set or reset a variable p to 2 if the second field
    # was found in the ids lookup
    p = 2
}

# Decrement the variable p on every iteration and check if it
# is greater than 0 after that. If that's true, awk will print 
# the current line
p--> 0

使用特定符号之间匹配的 ID 字符串过滤多 fasta 文件

Filter multi fasta file with matching ID string between specific symbols

bash

bioinformatics

biopython

fasta