Mishandling sequence headers with custom delimiters and ISO formatted dates

[ArtPoon]

Bug report from user:

python anchre.py  -sep ";" -ft2 /app/FastTree/2.1.8/bin/FastTree -R /app/bin/Rscript -java /app/java/jdk1.8.0_31/bin/java rv217_anon_1w_18.fasta rv217_1w/1w_18.fasta rv217_1w/1w_18.csv
fasttree2
rtt
Error in if (tp[3] != "") obj$node.label <- tp[3] :
 missing value where TRUE/FALSE needed
Calls: read.tree -> lapply -> FUN
Execution halted
root2tip
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
       at dr.app.tools.NexusExporter.exportTrees(Unknown Source)
       at dr.app.tools.NexusExporter.exportTrees(Unknown Source)
       at dr.app.pathogen.RLRootToTip.<init>(Unknown Source)
       at dr.app.pathogen.RLRootToTip.main(Unknown Source)
Traceback (most recent call last):
 File "anchre.py", line 477, in <module>
   main()
 File "anchre.py", line 429, in main
   res = anchre.call_root2tip(rooted)
 File "anchre.py", line 298, in call_root2tip
   out2], stdout=subprocess.PIPE)
 File "/fh/fast/edlefsen_p/tholzman/anaconda/lib/python2.7/subprocess.py", line 540, in check_call
   raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/app/java/jdk1.8.0_31/bin/java', '-jar', 'java/RLRootToTip.jar', '-timetree', '/tmp/anchre.r2t.timetree', '-newick', '/tmp/anchre-tmp', '/tmp/anchre.r2t.csv']' returned non-zero exit status 1

To avoid further confusion, let's change the data structure so that the original and custom sequence headers are stored by the same object.