https://stackoverflow.com/questions/32481877/what-is-nr-fnr-in-awk
Look for keys (first word of line) in file2 that are also in file1.
Step 1: fill array a with the first words of file 1:
awk '{a[$1];}' file1
Step 2: Fill array a and ignore file 2 in the same command. For this check the total number of records until now with the number of the current input file.
awk 'NR==FNR{a[$1]}' file1 file2
Step 3: Ignore actions that might come after } when parsing file 1
awk 'NR==FNR{a[$1];next}' file1 file2
Step 4: print key of file2 when found in the array a
awk 'NR==FNR{a[$1];next} $1 in a{print $1}' file1 file2
pony@z2air:/mnt/d/Biosoft/MCScanX/at$ head at.test
evm.model.fragScaff_scaffold_15.30
evm.model.fragScaff_scaffold_15.66
evm.model.fragScaff_scaffold_15.52
evm.model.fragScaff_scaffold_15.52
evm.model.fragScaff_scaffold_15.52
evm.model.fragScaff_scaffold_15.52
evm.model.fragScaff_scaffold_15.52
evm.model.fragScaff_scaffold_15.139
evm.model.fragScaff_scaffold_15.81
evm.model.fragScaff_scaffold_15.81
pony@z2air:/mnt/d/Biosoft/MCScanX/at$ head at.gff
fc15 evm.model.fragScaff_scaffold_15.18 172819 173259
fc15 evm.model.fragScaff_scaffold_15.30 314441 318368
fc15 evm.model.fragScaff_scaffold_15.109 1117575 1118396
fc15 evm.model.fragScaff_scaffold_15.140 1593997 1594908
fc15 evm.model.fragScaff_scaffold_15.66 684328 686553
fc15 evm.model.fragScaff_scaffold_15.52 540989 544116
fc15 evm.model.fragScaff_scaffold_15.96 1018996 1024259
fc15 evm.model.fragScaff_scaffold_15.139 1584325 1585666
fc15 evm.model.fragScaff_scaffold_15.7 46014 46783
fc15 evm.model.fragScaff_scaffold_15.81 814968 815669
$ awk 'NR==FNR{a[$1];next}$2 in a {print $1}' at.test at.gff >test
NR:
FNR:
a[$1]: evm.model.fragScaff_scaffold_15.18
$2: fc15 evm.model.fragScaff_scaffold_15.18
print $1: fc15
