[SOLVED] Print matches between two files and line after, while ordering by reference file

Issue

I have a ref file

NP_001041718.1
XP_021405980.1
NP_001041719.1
XP_021385112.1
NP_001041721.1
XP_021394530.1
NP_001041722.1
XP_021394327.1
NP_001041723.1
XP_021400667.1

I need to capture the matches plus next line in a target file that looks like this, keeping the order from the reference file

NP_001041718.1
DVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSRTKEGVVHGVTTVAEKTKEQVSNVGGAVVTGVTAVAQKTVEGAGNIAAATGLVKKDQLAKQNEEGFLQEGMVNNTGVAVDPENEAYEMPPEEEYQDYEPEA
NP_001041719.1
GKQNSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKSEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQCDPSSAGQF
NP_001041721.1
TMESGAENQQSGDAAGTEAETQQMTVQAQPQIATLAQVSMPAAHATSSAPTVTLVQLPNGQTVQVHGVIQAAQPSVIQSPQVQTVQISTIAESEDSQESVDSVTDSQKRREILSRRPSYRKILNDLSSDAPGVPRIEEEKSEEETAAPAIATVTVPTPIYQTSSGQYIAITQGGAIQLSNNGTDGVQGLQTLTMTNAAATQPGTTILQYAQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVMASSPALPTQPAEEAARKREVRLMKNREAARECRRKKKEYVKCLENRVAVLENQNKTLIEELKALKDLYCHKSD
NP_001041722.1
RVNESELNSSVLPRDPPAEGAPRRQPWVTSTLAAILIFTIAVDLLGNLLVILSVYRNKKLRNAGNVFVVSLAVADLIVAIYPYPLVLTSVFHNGWKLGYLHCQISGFLMGLSVIGSIFNITGIAINRYCYICHSLKYDKLYSDRNSLCYIVLIWLLTFVAIVPNLFVGSLQYDPRIYSCTFAQSVSSAYTIAVVFFHFLLPIAVVTFCYLRIWILVIQVRRRVKPDNNPRLKPHDFRNFVTMFVVFVLFAVCWAPLNFIGIAVAVNPKTVIPRIPEWLFVSSYYMAYFNSCLNAIVYGLLNQNFRREYKRIIVNFCTAKVFFQDSSNDAGDRMRSKPSPLITNNNQVKVDSV
NP_001041723.1
LENGSLRNCCDPGGRGRLGLAEREAAAAGAPRPAWVVPVLSSVLIFTTVVDILGNLLVILSVFKNRKLRNSGNAFVVSLALADLVVALYPYPLVLLAIFHNGWTLGETHCKASGFVMGLSVIGSIFNITAIAINRYCYICHSFAYDKVYSCWNTMLYVSLVWILTVIATVPNFFVGSLKYDPRIYSCTFVQTASSYYTIAVVVIHFIVPITIVSFCYLRIWVLVLQVRRRVKSETKPRLKPSDFRNFLTMFVVFVIFAFCWAPLNFIGLAVAIDPTEMAPKVPEWLFIISYLMAYFNSCLNAIIYGLLNQNFRNEYKRISMSLWMPRLFFQDTSKGGTDGQKSKPSPALNNNNQMKTETL
XP_021405980.1
DVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSRTKEGVVHGVTTVAEKTKEQVSNVGGAVVTGVTAVAQKTVEGAGNIAAATGLVKKDQLAKQNEEGFLQEGMVNNTGVAVGPENEAYKMPPEEEYQDYEPEA
XP_021385112.1
GKQNSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKSEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQCDPSSAGQF
XP_021394530.1
TMESGAENQQSGDAAGTEAETQQMTVQAQPQIATLAQVSMPAAHATSSAPTVTLVQLPNGQTVQVHGVIQAAQPSVIQSPQVQTVQISTIAESEDSQESVDSVTDSQKRREILSRRPSYRKILNDLSSDAPGVPRIEEEKSEEETAAPAIATVTVPTPIYQTSSGQYIAITQGGAIQLSNNGTDGVQGLQTLTMTNAAATQPGTTILQYAQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVMASSPALPTQPAEEAARKREVRLMKNREAARECRRKKKEYVKCLENRVAVLENQNKTLIEELKALKDLYCHKSD
XP_021394327.1
RVNESELNSSVLPRDPPAEGAPRRQPWVTSTLAAILIFTIAVDLLGNLLVILSVYRNKKLRNAGNVFVVSLAVADLIVAIYPYPLVLTSVFHNGWKLGYLHCQISGFLMGLSVIGSIFNITGIAINRYCYICHSLKYDKLYSDRNSLCYIVLIWLLTFVAIVPNLFVGSLQYDPRIYSCTFAQSVSSAYTIAVVFFHFLLPIAVVTFCYLRIWILVIQVRRRVKPDNNPRLKPHDFRNFVTMFVVFVLFAVCWAPLNFIGIAVAVNPKTVIPRIPEWLFVSSYYMAYFNSCLNAIVYGLLNQNFRREYKRIIVNFCTAKVFFQDSSNDAGDRMRSKPSPLITNNNQVKVDSV
XP_021400667.1
LENGSLRNCCDPGGRGRLGLAEREAAAAGAPRPAWVVPVLSSVLIFTTVVDILGNLLVILSVFKNRKLRNSGNAFVVSLALADLVVALYPYPLVLLAIFHNGWTLGETHCKASGFVMGLSVIGSIFNITAIAINRYCYICHSFAYDKVYSCWNTMLYVSLVWILTVIATVPNFFVGSLKYDPRIYSCTFVQTASSYYTIAVVVIHFIVPITIVSFCYLRIWVLVLQVRRRVKSETKPRLKPSDFRNFLTMFVVFVIFAFCWAPLNFIGLAVAIDPTEMAPKVPEWLFIISYLMAYFNSCLNAIIYGLLNQNFRNEYKRILMSLWMPRLFFQDTSKGGTDGQKSKPSPALNNNNQMKTETI

so the output would look like

    NP_001041718.1
    DVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSRTKEGVVHGVTTVAEKTKEQVSNVGGAVVTGVTAVAQKTVEGAGNIAAATGLVKKDQLAKQNEEGFLQEGMVNNTGVAVDPENEAYEMPPEEEYQDYEPEA
    XP_021405980.1
    DVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSRTKEGVVHGVTTVAEKTKEQVSNVGGAVVTGVTAVAQKTVEGAGNIAAATGLVKKDQLAKQNEEGFLQEGMVNNTGVAVGPENEAYKMPPEEEYQDYEPEA
    NP_001041719.1
    GKQNSKLRPEVMQDLLESTDFTEHEIQEWYKGFLRDCPSGHLSMEEFKKIYGNFFPYGDASKFAEHVFRTFDANGDGTIDFREFIIALSVTSRGKLEQKLKWAFSMYDLDGNGYISKSEMLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNRDGKLSLEEFIRGAKSDPSIVRLLQCDPSSAGQF
    XP_021385112.1
    ....

I know how to find the matches in target while keeping the order from ref awk 'FNR==NR {a[$1]=$0; next}; $1 in a {getline} {print a[$1]}' target ref , but I don't know how to print the line after. I know how to print the line after with grep -A 1 -f ref target, but it reorders the target file

Solution

Would you please try the following:

awk 'FNR==NR {                          # process "target" file
    if (FNR%2) a[key=$1]=$0             # store odd lines in array a
    else b[key]=$0                      # store even lines in array b using the same key as the previous line
    next
}
$1 in a {print a[$1]; print b[$1]}      # if the key matches, print the odd line and the even line
' target ref

Answered By - tshiono

Answer Checked By - Clifford M. (WPSolving Volunteer)