Help with python code to search string in one file & replace with line in other file

[Larz60+]

Questions:

• The only thing you want to replace are the headers, not the data, correct?
  
• Also, the header text does not match exactly between files:
  

  Output:
  Original: Clavigralla_tomentosicollis_gi_512427643_gb_GAJX01006991.1[b]_0_rc[/b]
  Replacement: Clavigralla_tomentosicollis_gi_512427643_gb_GAJX01006991.1

• How much is necessary to create unique match (I am assuming anything after the '.' is not part of the match)
  

Almost there give me another hour or so.