selenocysteines are not being replaced

[guyleonard]

I have a sed command that is supposed to check for selenocysteine (U) and other junk in the sequence files of each run - as MAFFT has a hissy fit when it sees them and the "--anysymbol" seems to produce shit alignments. The consequence is zero-sized files and then downstream programs quit/crash and then the pipeline fails. needs to be sorted! 1) make sure the U and non-IUPAC protein codes are repalced by X and 2) fail gracefully!!!!!

[guyleonard]

the | is potentially causing issues!?

        # sed -i '/^>/!s/U/X/g' *.fas - works fine...