damurdock
commented
6 years ago Thank you for the heads-up on the first issue, I'll update the documentation to reflect the current state of SIDR.
As for the second issue, I believe this is the result of an older version of PySAM being used. Version 0.8.1 of PySAM introduced the method that SIDR uses to create file objects, and SIDR's setup script does not yet enforce a minimum version. Therefore, if an older version of PySAM was already installed on your machine, installing SIDR wouldn't update it and could result in that error. I'll update the setup script for SIDR to enforce a minimum version of PySAM so this will be avoided in the future.
Can you run the following command on the machine where SIDR is installed and tell me what it returns? python -c "import pysam; print(pysam.__version__)" If that returns something older than 0.8.1, running pip install --upgrade pysamshould fix the issue you're seeing. If you're running other software that doesn't work with the newer versions of PySAM, you can install SIDR in a virtualenv.
Thank you, Duncan
muszewska
The list of arguments differs in documentation and program
sidr default -d [taxdump path] -b [bamfile] -f [assembly FASTA] -r [BLAST results] -m model.dot -k tokeep.contigids -x toremove.contigids -t [target phylum]
Error: no such option: -m
reading in BAM file: Traceback (most recent call last): File "/usr/local/bin/sidr", line 11, in
sys.exit(cli())
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 722, in call
return self.main(args, kwargs)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 535, in invoke
return callback(args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/sidr/cli.py", line 54, in default_runner
default.runAnalysis(bam, fasta, blastresults, taxdump, modelOutput, output, tokeep, toremove, binary, target, level)
File "/usr/local/lib/python2.7/dist-packages/sidr/default.py", line 106, in runAnalysis
contigs = readBAM(bam, contigs)
File "/usr/local/lib/python2.7/dist-packages/sidr/default.py", line 46, in readBAM
alignment = pysam.AlignmentFile(BAMFile, "rb")
AttributeError: 'module' object has no attribute 'AlignmentFile'