Changes special characters in samples names from incoming matrix file

[spacocha]

dbOTUcaller.py changes the headers if the headers contain periods (probably spaces or other characters too). Underscores (_) seem to be ok. This can create an issue with down stream analysis because you have different samples names than you thought. Make a pre-flight check in SmileTrain and dbOTUcaller.py which identifies this error and doesn't continue unless it's fixed.

[swo]

Does this happen because you load the table in R? If so, R's read.table function has a check.names option, which you can set to FALSE to keep whatever was in the file. Let as TRUE, the default, it would change 1234 to X1234, A+B to A.B, etc.