How to used grep to match exact words-CodePudding

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_ID.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.

CodePudding user response：

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
      }
}' words.lst file.csv

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

CodePudding user response：

It looks like you're always matching field 3. 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" '$3 == i' metexplore_IDs_DB.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} 
    $5 in houses' corrected_inhouse_list.txt metexplore_IDs_DB.tsv