How to used grep to match exact words

Question

I have an list/array in zsh which is house=$(cat corrected_inhouse_list.txt)

Containing:

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

File "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

And I want to use grep to match this words on a file. The Problem is what one can see in the picture, grep also captures words that contain but not start with my word of interes.

I've tried:

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

What can I do to achieve my goal? the desired output would be without lines 57, 95, 107 and 237.

Answer 1

It looks like you're always matching field 4. So awk would be a better solution, since you can simply do an exact match with the whole field:

for i in "${house[@]}"; do
    awk -F'\t' -v i="$i" '$4 == i' metexplore_ID.tsv
done

Don't forget the quotes around ${house[@]} ; otherwise elements like L-GLUTAMIC ACID will be treated as two different words to match.

You can also avoid creating the array and looping by loading corrected_inhouse_list.txt directly into an awk array:

awk -F'\t' -v i="$i" '
    NR == FNR {houses[$0]++; next} 
    $4 in houses' corrected_inhouse_list.txt metexplore_ID.tsv

Answer 2

You may comside this awk that builds regex for each entry from your list and then searches that regex anywhere in the csv file:

awk '
NR == FNR {
   kw[ "(^|[[:blank:]])" $0 "([[:blank:]]|$)" ]
   next
}
{
   for (w in kw)
      if ( $0 ~ 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