gilesc/BioTK — pull request #5 by glennsb (2014-03-20 23:03:00+00:00)
Title: Fixes crash when trying to cast . into floats

The bed file being used had . in the score column, which made the
float() angry. This is just a quick/bad hack of make it shut up fix to
make any . turn into 0 instead, who really knows if that is the score
one wants or if really it would be better to have no score in that case,
probably no score, but what can you do these days with the kids and
their cellphones

Users were experiencing errors in RepeatSoaker.py with an "rmsk" bed file built from its code, ala:

```
File "/usr/local/analysis/repeatsoaker/20140320/bin/RepeatSoaker.py", line 97, in
main(sys.argv[1:])
File "/usr/local/analysis/repeatsoaker/20140320/bin/RepeatSoaker.py", line 42, in main
for region in h:
File "/usr/local/analysis/biotk/0.0.1-17-ga1f0c30/lib/python3.3/site-packages/BioTK/io/BED.py", line 21, in __iter__
attrs["score"] = float(attrs["score"])
ValueError: could not convert string to float: '.'
```

Offending bed file has "." in the score column, ala

```
chrY 59353683 59353825 L2a . -
chrY 59355988 59356025 (CCA)n . +
chrY 59356896 59356947 GA-rich . +
chrY 59357385 59357476 MIR3 . +
```

Perhaps the BED file is wrong, perhaps the . shouldn't be a zero & instead should be skipped, for now I zeroed the score just so the float() cast would still get called. This could be done much better