artpoon/anchre

Code for the Gates/RSA methods bakeoff

anchre's Issues

check_call failing to return from running BEAST jar

This causes the anchre process to hang.

Mishandling sequence headers with custom delimiters and ISO formatted dates

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.

Cannot specify initial root height for starting tree in BEAST 1.8.x

This functionality appears to be broken in BEAST, insofar as I specified an initial value for a uniform prior on rootHeight using the BEAUTI interface, and that value was no where to be found in the resulting XML output. However, this appears to affect the random (coalescent) starting tree. Using UPGMA to generate an initial tree seems to be okay.