so I have found a question on here that is the opposite of what I would like to do here: Concatenate multiple files with same header.
I am trying to merge or concatenate 2 files,within a directory within hundred of files that have a counterpart file with the same substring, into one file based on the '>' character in the header. There are thousands of headers within the each file and as opposed to the question asked in the link I attached, the contents other than the header are the same so I don't want to change anything but every line that begins with '>'.
Essentially I would like to combine file1 to file2 by the shared character '>' and to leave the contents of file 1 in order.
File1 > MGBNCNOSNC_142 9u2o4840204a9 > MGBNCNOSNC_143 AOISCJNWDCSNDCCW > MGBNCNOSNC_144 AOISCJ40204DZZW
File2 >King_Henry >Queen_jerry >Jack_jill
Output > MGBNCNOSCNC_142 > King_henry 9u2o4840204a9 > MGBNCNOSCNC_143 > Queen_jerry AOISCJNWDC > MGBNCNOSNC_144 > Jack_jill gefSCJ40204DZZW
Thanks for any help and let me know if I can be any clearer!