Umm, I said "If each file really is "straight text, no carriage returns, no spaces, etc. " If there are no carriage returns there is only one line. If you are getting the file name every other line than your file has one more than one line and doesn't fit the requirement straight text, no carriage returns, no spaces, etc. Also, no where is it specified to remove the ".txt". In fact the example specifically shows the ".txt" being there

filename: a36.txt
initial filecontents :

AATGACGTACGTAGTCGTAGCGT

after script filecontents :

>a36.txt
AATGACGTACGTAGTCGTAGCGT
[newline]
[download]