如何使用 grep 来匹配精确的单词

Question

我在 zsh 中有一个 list/array，它是 house=$(cat corrected_inhouse_list.txt)

包含：

N-METHYL-L-GLUTAMIC ACID
L-GLUTAMIC ACID
CREATINE
L-PROLINE
CREATINE PHOSPHATE
L-VALINE
L-TYROSINE
L-KYNURENINE
L-PHENYLALANINE
PHENYLETHANOLAMINE
D-PANTOTHENIC ACID
L-TRYPTOPHAN
MYRISTIC ACID

文件“metexplore_IDs_DB.tsv”：

8:M_Lkynr   exact multimatching 1   L-KYNURENINE    CHEBI:16946 NA  NA
21:M_glu_L  exact multimatching 1   L-GLUTAMIC ACID CHEBI:16015 NA  NA
40:M_trp_L  exact multimatching 1   L-TRYPTOPHAN    CHEBI:16828 NA  NA
42:M_pro_L  exact multimatching 1   L-PROLINE   CHEBI:17203 NA  NA
50:M_phe_L  exact multimatching 1   L-PHENYLALANINE CHEBI:17295 NA  NA
56:M_creat  exact multimatching 1   CREATINE    CHEBI:16919 NA  NA
57:M_34dhphe    exact multimatching 1   3,4-DIHYDROXY-L-PHENYLALANINE (L-DOPA)  CHEBI:15765 NA  NA
61:M_tyr_L  exact multimatching 1   L-TYROSINE  CHEBI:17895 NA  NA
63:M_val_L  exact multimatching 1   L-VALINE    CHEBI:16414 NA  NA
94:M_Lkynr  exact multimatching 1   L-KYNURENINE    CHEBI:16946 NA  NA
95:M_5oxpro exact multimatching 1   5-OXO-L-PROLINE CHEBI:18183 NA  NA
107:M_4hpro_LT  exact multimatching 1   4-HYDROXY-L-PROLINE CHEBI:18095 NANA
171:M_pcreat    exact multimatching 1   PHOSPHOCREATINE CHEBI:17287 NA  NA
191:M_pnto_R    exact multimatching 1   D-PANTOTHENIC ACID  CHEBI:7916  NANA
211:M_pcreat    exact multimatching 1   CREATINE PHOSPHATE  CHEBI:17287 NANA
237:M_35diotyr  exact multimatching 1   3,5-DIIODO-L-TYROSINE   CHEBI:15768 NANA
315:M_ttdca exact multimatching 1   MYRISTIC ACID   CHEBI:28875

而且我想使用 grep 来匹配文件中的这个词。问题是在图片中可以看到什么，grep 还会捕获包含但不以我感兴趣的单词开头的单词。

我试过：

for i in ${house[*]}; do grep -n -E "^\s*\{$i}\>" metexplore_IDs_DB.tsv; done
for i in ${house[*]}; do grep -n -E -w "\<$i" metexplore_IDs_DB.tsv; done 
for i in ${house[*]}; do grep -n -E "(^|\t)$i" metexplore_IDs_DB.tsv; done

我可以做些什么来实现我的目标？所需的输出将没有第 57、95、107 和 237 行。

Answer 1

看起来你总是匹配字段 4。所以 awk 会是一个更好的解决方案，因为你可以简单地对整个字段进行精确匹配：

for i in "${house[@]}"; do
    awk -F'\t' -v i="$i" ' == i' metexplore_ID.tsv
done

不要忘记 ${house[@]} 两边的引号；否则像 L-GLUTAMIC ACID 这样的元素将被视为两个不同的词来匹配。

您还可以通过将 corrected_inhouse_list.txt 直接加载到 awk 数组来避免创建数组和循环：

awk -F'\t' -v i="$i" '
    NR == FNR {houses[[=11=]]++; next} 
     in houses' corrected_inhouse_list.txt metexplore_ID.tsv

Answer 2

您可以考虑这个 awk 为列表中的每个条目构建正则表达式，然后在 csv 文件中任何地方 搜索该正则表达式：

awk '
NR == FNR {
   kw[ "(^|[[:blank:]])" [=10=] "([[:blank:]]|$)" ]
   next
}
{
   for (w in kw)
      if ( [=10=] ~ w ) {
         print
         next
      }
}' corrected_inhouse_list.txt metexplore_ID.tsv

i8:M_Lkynr   exact multimatching 1   L-KYNURENINE    CHEBI:16946 NA  NA
21:M_glu_L  exact multimatching 1   L-GLUTAMIC ACID CHEBI:16015 NA  NA
40:M_trp_L  exact multimatching 1   L-TRYPTOPHAN    CHEBI:16828 NA  NA
42:M_pro_L  exact multimatching 1   L-PROLINE   CHEBI:17203 NA  NA
50:M_phe_L  exact multimatching 1   L-PHENYLALANINE CHEBI:17295 NA  NA
56:M_creat  exact multimatching 1   CREATINE    CHEBI:16919 NA  NA
61:M_tyr_L  exact multimatching 1   L-TYROSINE  CHEBI:17895 NA  NA
63:M_val_L  exact multimatching 1   L-VALINE    CHEBI:16414 NA  NA
94:M_Lkynr  exact multimatching 1   L-KYNURENINE    CHEBI:16946 NA  NA
191:M_pnto_R    exact multimatching 1   D-PANTOTHENIC ACID  CHEBI:7916  NANA
211:M_pcreat    exact multimatching 1   CREATINE PHOSPHATE  CHEBI:17287 NANA
315:M_ttdca exact multimatching 1   MYRISTIC ACID   CHEBI:28875

如何使用 grep 来匹配精确的单词

How to used grep to match exact words

linux

bash

zsh