#250 Improve "No search paths found!" error message

[William S Noble]

The following command

/net/noble/vol1/home/noble/proj/crux/trunk/src/crux assign-confidence\
--estimation-method tdc --score "exact p-value" --smaller-is-better T --overwr\
ite T --output-dir foobar foo

yields the error message: "No search paths found!" The meaning of this cryptic error message is completely opaque. After some investigating, it seems that it's related to the fact that the filename has no extension. I think assign-confidence is trying to do some kind of substitution to look for the word "target" and replace it with "decoy." This shouldn't be necessary because the output file contains concatenated results. Furthermore, the error message should read something like, "No decoys found in 'foo' and no decoy file specified."

[William S Noble]

I ran into this error message in a different context, where I had mistyped the name of the input file to assign-confidence. This implies that perhaps the error is not related to searching for a sibling decoy file. Perhaps the error message is simply supposed to read "Cannot open file 'foo'."