Not a oneliner, but maybe slightly better readable...

#!/usr/bin/perl

# create names lookup table from first file
while (<>) {
    $names{$_} = 1;
    last if eof;
}

$/ = "\n>";  # set input record separator

# scan second file
while (<>) {
    print if /^>?(\w+\n)/ && $names{$1};
}
[download]

Usage:

$ ./extract.pl file1 file2 >output
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Update: you could of course also make a oneliner out of it :)

$ perl -ne'$/eq"\n"?$nm{$_}++:/^>?(\w+\n)/&&$nm{$1}&&print;$/="\n>"if 
+eof' file1 file2 >output
[download]

Or (approaching the realms of golfing and obfu):

$ perl -ne'1..eof&&($/=">")?${$_}++:/.+\n/&${$&}&&print' file1 file2 >
+output
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Thanks a lot, your script is great. Your solution is also a lot faster than the awk oneliner. I modified it a bit to fit my real data.



#!/usr/bin/perl

# create names lookup table from first file
while (<>) {
    #get rid of newline in name because there might be 
    #something like >name1\stext\n in the second file
    chomp;
    $names{$_} = 1;
    last if eof;
}
$/ = "\n>";  # set input record separator

# scan second file
print ">";            # print first ">" that would be missing
while (<>) {
      
    print if /^>?([\w\d]+)/ && $names{$1};
}
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The only prob I have now is, when applied to my real data a ">" sign is missing at the beginning (which I got around with a print before the second while loop) and one is too much at the end.

The only prob I have now is, when applied to my real data a ">" sign is missing at the beginning ... and one is too much at the end.

The reason for this is the way the records are being split. The first record (and only the first) will have a leading ">", and all records except for the last will have a trailing ">". Now, if you happen to not print out the first record (because it doesn't match) the initial ">" will be missing from the output file. Similarly, if you happen to not print the last record, there will be a stray ">" from the previous record.

The proper way to handle those corner cases would be to always remove any leading or trailing ">"s, and always add a new one for output:

...
# scan second file
while (<>) {
    s/^>//;  # remove leading  '>'
    s/>$//;  # remove trailing '>'

    print ">$_" if /^([\w\d]+)/ && $names{$1};
    #  add ^
}
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(This way, you also no longer need to allow a leading ">" in the regex (the >? part). )

I don't find: "awk 'NR==FNR {a$1;next} $1 in a {print RS$0}' file1 RS=">" file2 > output" easy to understand.

The output swaps the data associated with >name1 and >name3.

Note, that the output shown in OP is incorrect. Actual output will be:

>name3
text text
text text

>name1
some kind 
of text
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So it doesn't swap anything.

Right, my mistake. Though the order of output is not important to me in this case.