Shell Programming and Scripting

Hi guys,
I have a problem please help if you have any solutions.

I have two files. FILE1 having records separated by '>'

FILE1
>LOG_Ps04g30040.1|12004.m08110|test lc-like prot, test1
MGASPSREEAHSNSSFSGNGKAMAVASSASSSGSNQAQSKRAPALHMFQEIVAEKDFTAS
LPKQ*
>ab|22329085|xyz|PP_194957.2| (CALRE);on biding [liana]
MGLPQNKLSFFCFFFLVSVLTLAPLAFSEIFLEEHFEGGWKSRWVLSDWKRNEGKAGTFKHTAGKWPGD
DNKGIQTYNDAKHYAISAKIPEFSNKNRTLVVQYSVKIEQDIECGGAYIKLLSGYVNQKQFGGDTPYSL
HDEL
>pnl_A5C9U1_VITVI A7Q0M0 chr scaffold_42,shotgun
MKLLSGEVDQKKFGGDTPYSIMFGPDICGYSTKKVHAIFSYQGSNHLIKKDVPCETDQLT
HVYTFVLRPDATYSILIDNVEKQSGSLYSDWDILPPKQIKDAKAKKPEAWDDKEYIPDPE
WKAPMIDNPDFKDDPDFFIYPHLKYVGIELWQVKSG*TMFDNILVCDDPDYAKKLAEETW
KHKGAEKTAFEEQEKKREEEESKDDPDDSDVSSIKSLPGFH
>Glyta16g22680.1
MSFEDSSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRK
KVKSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRKTIK
NAKKPEDWDDREYIDDPNDVKPEGFDSIPREIPDRKAKEPEDWDEEENGLWEPPKIPNSA
>cgi|Poptr1_1|555048|eu3.00031681 on binding [test2]
MGLPQNKLSFFCFFFLVSVLTLAPLAFSEIFLEEHFEGGWKSRWVLSDWKRNEGKAGTFKHTAGKWPGD
DNKGIQTYNDAKHYAISAKIPEFSNKNRTLVVQYSVKIEQDI

I want to arrange the records in the same order as they are in FILE2. It only contains the text before the first space in the line containing '>'.

FILE2
cgi|Poptr1_1|555048|eu3.00031681
pnl_A5C9U1_VITVI
ab|22329085|xyz|PP_194957.2|
Glyta16g22680.1
LOG_Ps04g30040.1|12004.m08110|test

The OUTPUT should be like this -

>cgi|Poptr1_1|555048|eu3.00031681 on binding [test2]
MGLPQNKLSFFCFFFLVSVLTLAPLAFSEIFLEEHFEGGWKSRWVLSDWKRNEGKAGTFKHTAGKWPGD
DNKGIQTYNDAKHYAISAKIPEFSNKNRTLVVQYSVKIEQDI
>pnl_A5C9U1_VITVI A7Q0M0 chr scaffold_42,shotgun
MKLLSGEVDQKKFGGDTPYSIMFGPDICGYSTKKVHAIFSYQGSNHLIKKDVPCETDQLT
HVYTFVLRPDATYSILIDNVEKQSGSLYSDWDILPPKQIKDAKAKKPEAWDDKEYIPDPE
WKAPMIDNPDFKDDPDFFIYPHLKYVGIELWQVKSG*TMFDNILVCDDPDYAKKLAEETW
KHKGAEKTAFEEQEKKREEEESKDDPDDSDVSSIKSLPGFH
>ab|22329085|xyz|PP_194957.2|(CALRE);on biding [liana]
MGLPQNKLSFFCFFFLVSVLTLAPLAFSEIFLEEHFEGGWKSRWVLSDWKRNEGKAGTFKHTAGKWPGD
DNKGIQTYNDAKHYAISAKIPEFSNKNRTLVVQYSVKIEQDIECGGAYIKLLSGYVNQKQFGGDTPYSL
HDEL
>Glyta16g22680.1
MSFEDSSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRK
KVKSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRKTIK
NAKKPEDWDDREYIDDPNDVKPEGFDSIPREIPDRKAKEPEDWDEEENGLWEPPKIPNSA
>LOG_Ps04g30040.1|12004.m08110|test lc-like prot, test1
MGASPSREEAHSNSSFSGNGKAMAVASSASSSGSNQAQSKRAPALHMFQEIVAEKDFTAS
LPKQ*

Thanks

Code:

awk -v ORS= 'NR==FNR{a[$1]=$0;next}$0=">"a[$0]' RS='>' file1 RS='\n' file2

Thanks Rubin, there is a small error in the output.

The output I am getting is -
>cgi|Poptr1_1|555048|eu3.00031681 on binding [test2]
MGLPQNKLSFFCFFFLVSVLTLAPLAFSEIFLEEHFEGGWKSRWVLSDWKRNEGKAGTFKHTAGKWPGD
DNKGIQTYNDAKHYAISAKIPEFSNKNRTLVVQYSVKIEQDI


>pnl_A5C9U1_VITVI A7Q0M0 chr scaffold_42,shotgun
MKLLSGEVDQKKFGGDTPYSIMFGPDICGYSTKKVHAIFSYQGSNHLIKKDVPCETDQLT
HVYTFVLRPDATYSILIDNVEKQSGSLYSDWDILPPKQIKDAKAKKPEAWDDKEYIPDPE
WKAPMIDNPDFKDDPDFFIYPHLKYVGIELWQVKSG*TMFDNILVCDDPDYAKKLAEETW
KHKGAEKTAFEEQEKKREEEESKDDPDDSDVSSIKSLPGFH
>>Glyta16g22680.1
MSFEDSSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRK
KVKSKKHQSVGPWGGNGGSRWDDGIYSGVRQLVIVHGTGIDSIQIEYDKKGSSIWSEKHGGSGGRKTIK
NAKKPEDWDDREYIDDPNDVKPEGFDSIPREIPDRKAKEPEDWDEEENGLWEPPKIPNSA
>LOG_Ps04g30040.1|12004.m08110|test lc-like prot, test1
MGASPSREEAHSNSSFSGNGKAMAVASSASSSGSNQAQSKRAPALHMFQEIVAEKDFTAS
LPKQ*

one entry is missing and there is a new line between first and second record and also there is an extra '>' in the third entry.

Thanks again and I'll be happy if u can explain the code specially what " -v ORS= " does.

The code works fine, with the same output as your first post, either with old awk or gawk - tested. If it works for some entries, it should work for all them.
I'm assuming the files' formation looks exactly as your samples, but I doubt that file2 is not an exact copy of the first field of file1, at least for some entries, maybe it has extra characters, doublecheck to make sure.
-v ORS= set output record separator to the null string ( default is a newline, ORS="\n" ) .

Thanks, Ya there was some difference in characters but still an empty line is introduced after the first record in the output file.