BuildTrees error handling if SEQUENCE_ID contains commas or parentheses

[Roy Jiang]

Example of a changeo file containing SEQUENCE_ID’s with commas attached.

Recommendations: 1. warn users if they have commas/parentheses/long names and say that the program does not accept this. 2. come up with a system so that igphyml can accept long names, names with comas/parentheses by pre-processing the data in python before submitting to igphyml maybe using a hashmap. Your users would greatly appreciate #2.

[Kenneth Hoehn]

Fixed. See latest commit (701c506). It just translates all commas and parentheses in the sequence ID and --md fields to a dash (-). A hashmap would require outputting another file, and modifying readIgphyml in Alakazam to take it in. I’ll save that for another time.

Also, csv? Boo.

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