使用文件 2 中的键值对 bash 将值附加到文件 1 中

问题描述 投票：0回答：1

我见过很多版本的类似问题，但使用 bash 的不是一个好的版本（除非我错过了，请指导我找到一个）。

我需要通过将 

file1.txt
中的键匹配到 
keyvalue.txt
中找到的相同键来附加值。

文件格式如下：

file1.txt
其中包含第 10 列中的“taxid”KEY（在物种名称之前）。

1e470705074f483368a70ad18a7,gi|296972128|gb|HM278533.1|,249,1309,100,237,98.394,1.37e-118,438,0,Uncultured,bacterium clone ncd557a11c1 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|2259146620|emb|OW925276.1|,249,363,100,237,98.394,1.37e-118,438,0,uncultured,Anaerolineae bacterium DNA containing 16S-23S intergenic spacer region, clone 43
29ec61e470705074f483368a70ad18a7,gi|1771871051|emb|LR646018.1|,249,1412,100,228,97.189,1.38e-113,422,253,uncultured,bacterium partial 16S rRNA gene
29ec61e470705074f483368a70ad18a7,gi|1271843868|gb|MG277305.1|,249,363,100,225,96.787,6.40e-112,416,253,Uncultured,bacterium clone OTU_3084 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|1271845089|gb|MG278526.1|,249,363,98,192,93.004,1.42e-93,355,253,Uncultured,bacterium clone OTU_4378 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|378812876|gb|JQ408060.1|,249,1299,100,192,92.369,1.42e-93,355,43,Uncultured,bacterium clone SEV1BE061 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|151655702|gb|EU012237.1|,249,1030,100,189,91.968,6.59e-92,350,43,Uncultured,Chloroflexi bacterium clone 251 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|440507165|gb|KC001159.1|,249,1308,100,189,92.000,6.59e-92,350,0,Unidentified,marine bacterioplankton clone P3-1B_21 16S ribosomal RNA gene, partial sequence
29ec61e470705074f483368a70ad18a7,gi|2259561892|emb|OW932746.1|,249,363,100,186,91.566,3.07e-90,344,391,uncultured,Anaerolineae bacterium DNA containing 16S-23S intergenic spacer region, clone 43
29ec61e470705074f483368a70ad18a7,gi|165972207|dbj|AB257651.1|,249,1468,100,186,91.700,3.07e-90,344,391,Uncultured,Chloroflexus sp. gene for 16S rRNA, partial sequence, clone: Dolo_29


keyvalue.txt
：

0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli
21,Bacteria,Pseudomonadota,Alphaproteobacteria,Caulobacterales,Caulobacteraceae,Phenylobacterium,Phenylobacterium immobile
33,Bacteria,Myxococcota,Myxococcia,Myxococcales,Myxococcaceae,Myxococcus,Myxococcus fulvus
35,Bacteria,Myxococcota,Myxococcia,Myxococcales,Myxococcaceae,Corallococcus,Corallococcus macrosporus
41,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Stigmatella,Stigmatella aurantiaca
43,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Cystobacter,Cystobacter fuscus
253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
254,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indoltheticum
391,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium sp.
396,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium phaseoli

期望的结果只是将从 

keyvalue.txt
开始的整行（键和值）附加到其中具有相同键 ID 的行的末尾（从第 10 列开始）。我一直在尝试从 
file1.txt
获取密钥，但由于某种原因，我保存了额外的值，因此我无法正确地从 
keyvalue.txt
中提取值。

这是我一直在尝试的方法，但效果不佳：

for line in $(cat file1.txt); do key=$( echo $line | cut -d"," -f10); \
if grep $key keyvalue.txt; then grep $key keyvalue.txt; fi; done

但是我得到了很多奇怪的输出，它在 grep 错误的键，并且基本上只是返回我的整个 

keyvalue.txt
，其中只有很多奇怪的空格，这真是一团糟。我认为因为物种名称（第 10 列之后的所有内容）带有额外的逗号，因此导致了此类问题，即使只是呼应这些行也会导致一些奇怪的事情发生。

例如（只需在文件中的另一随机行上进行测试）：

 for line in $(cat file1.txt); do echo $line; done

输出：

29ec61e470705074f483368a70ad18a7,gi|165972207|dbj|AB257651.1|,249,1468,100,186,91.700,3.07e-90,344,391,Uncultured,Chloroflexus
sp.
gene
for
16S
rRNA,
partial
sequence,
clone:
Dolo_29

当它应该是：

29ec61e470705074f483368a70ad18a7,gi|165972207|dbj|AB257651.1|,249,1468,100,186,91.700,3.07e-90,344,391,Uncultured,Chloroflexus sp. gene for 16S rRNA, partial sequence, clone: Dolo_29

我的理想输出就是（可以是一个单独的文件，它甚至不需要附加到 file1.txt，我可以稍后自己单独附加它）：

0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli 0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli
253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
43,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Cystobacter,Cystobacter fuscus
43,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Cystobacter,Cystobacter fuscus
0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli  
391,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium sp.
391,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium sp.
bash
1个回答
0
投票

在@markp-fuso的帮助下，这是一个对我有用的解决方案：

while read -r line; do key=$( echo $line | cut -d"," -f10); if grep -wq "^${key}" keyvalue.txt; then grep "^${key}" keyvalue.txt; fi; done < file1.txt

Output:

    0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli
    0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli
    253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
    253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
    253,Bacteria,Bacteroidota,Flavobacteriia,Flavobacteriales,Weeksellaceae,Chryseobacterium,Chryseobacterium indologenes
    43,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Cystobacter,Cystobacter fuscus
    43,Bacteria,Myxococcota,Myxococcia,Myxococcales,Archangiaceae,Cystobacter,Cystobacter fuscus
    0,Bacteria,Pseudomonadota,Gammaproteobacteria,Enterobacterales,Enterobacteriaceae,Escherichia,Escherichia coli
    391,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium sp.
    391,Bacteria,Pseudomonadota,Alphaproteobacteria,Hyphomicrobiales,Rhizobiaceae,Rhizobium,Rhizobium sp.

希望对其他有类似问题的人有帮助。

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