File 1 looks ilke this:-
12345   14
67890   21

File 2 looks like this:-
>gi|12345|ref|OM_2343434|Some text ...
ABCDEFANADEFGHIJKLMNOPQRSTVVWXWZ
>gi|67890|ref|HM_2338373|Some text ...
ABACFHAYJAYAFANJAKALAHUSSGSJISUSSKSOWUWSLSS

output should be like this:-
12345  11  FGH    
67890  21  ALA

Also the File 1 position character should be made bold.