Unknown Error running GESS

Question

[jjrin]

Hello Biostars, I am trying to run GESS with my data and this error keeps appearing:

/Library/Python/2.7/site-packages/Bio/Seq.py:345: BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead of my_seq.tostring().
  BiopythonDeprecationWarning)
Traceback (most recent call last):
  File "GESS.py", line 122, in <module>
    main()
  File "GESS.py", line 60, in main
    global_data = GESS_graphBuild(options,global_data)
  File "/Users/User1/Downloads/Software/gess/impl/SpliceSiteGraphProc.py", line 145, in GESS_graphBuild
    chr_ssgraph,chr_depthdict = ssGraphProc.process()
  File "/Users/User1/Downloads/Software/gess/impl/SpliceSiteGraphProc.py", line 53, in process
    self.chromSplicGraphMap = self.updateToDiGraph()
  File "/Users/User1/Downloads/Software/gess/impl/SpliceSiteGraphProc.py", line 103, in updateToDiGraph
    refseq = SeqIO.parse(genomedir + chrid + '.fa','fasta').next()

I have the latest version of Biopython and all of the packages necessary to run GESS. The program runs for five minutes but runs into this error. My bam file is indexed and all of the chromosomes are in individual fasta files in given directory. Thank you so much for the help!

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

This looks like a warning - does the script create output or not at all? Based on the warning there is something wrong in the script, not in your input. The script uses a method which is deprecated by Biopython. This should be easy to fix.

There is a call to my_seq.tostring() [probably not actually called my_seq] which should be changed to str(my_seq). I can't find the script online, GESS brings up too many hits.

[jjrin]

I checked some of the scripts that is referenced in the main code and I found a couple of instances of the str() problem. It runs now but gets stuck because there aren't enough threads even though I am sure that there are plenty on the powerful computer I am using. I know you aren't supposed to ask a completely new question here so I think I will open a new post on it. But thank you for your help!

    Traceback (most recent call last):
  File "GESS.py", line 122, in <module>
    main()
  File "GESS.py", line 62, in main
    global_data = GESS_exonSkipScanning(options,global_data)
  File "/Users/margaretsaha/Downloads/Software/gess/impl/ExonSkipScanProc.py", line 191, in GESS_exonSkipScanning
    global_data = exonSkipScanProc.process()
  File "/Users/margaretsaha/Downloads/Software/gess/impl/ExonSkipScanProc.py", line 47, in process
    t.start() ##
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 745, in start
    _start_new_thread(self.__bootstrap, ())
thread.error: can't start new thread