Question: Platypus variant caller error
0
gravatar for User000
11 weeks ago by
User000440
User000440 wrote:

Dear all,

I am trying to run Platypus variant caller but it continues to give me the following error:

print "\n\n%s command is not yet implemented\n\n" %(x) ^ SyntaxError: invalid syntax

Could you, please, suggest is there a way to solve this?

snp variant calling • 123 views
ADD COMMENTlink written 11 weeks ago by User000440

Hi, Seems like you are passing an argument to Platypus which it is unable to execute/ implement. If you can post the run set-up, then a better guess can be taken. The error message alone is not enough.

ADD REPLYlink written 11 weeks ago by Amitm2.1k

Thanks for the reply. This is the Platypus.py code. Could it be useful?

#!/usr/bin/env python

"""
Top-level interface to the Platypus tool-set
"""
from __future__ import division

import sys
import runner

###################################################################################################

def notImplemented(x):
    """
    Print an error message and raise an exception for commands that are not yet
    implemented.
    """
    print "\n\n%s command is not yet implemented\n\n" %(x)
    sys.exit(0)

###################################################################################################

if __name__ == "__main__":

    possCommands = {}
    possCommands["callVariants"] = runner.callVariants
    possCommands["continueCalling"] = runner.continueCalling

    if len(sys.argv) == 1 or sys.argv[1] not in possCommands.keys():
        print "\n\n"
        print "Invalid usage: use Platypus as follows:"
        print "\n"
        for k in possCommands.keys():
            print "python Platypus.py", k, "[Options]"
        print "\n"
        print "For a list of possible options for a specific command, type 'python Platypus.py Command -h'"
        print "\n"
        sys.exit(0)
    if sys.version_info[0] != 2 or sys.version_info[1] < 6:
        print "\n\n"
        print "Platypus works only with Python versions 2.6 and greater. Python 3.X is not yet supported."
        print "\n\n"
        sys.exit(0)
    else:
        command = sys.argv[1]
        possCommands[command](sys.argv[2:])
ADD REPLYlink written 11 weeks ago by User000440

I am running it as python Platypus.py

ADD REPLYlink written 11 weeks ago by User000440
1

Hi, I am sorry, no clue with the setup you are using for Platypus. I had followed the instructions here and was able to run it successfully (ver. 0.8.1).

After installation as specified, I used this setup -

##
## HTSLib path needed
export C_INCLUDE_PATH=/software/packages/htslib/1.4/include
export LIBRARY_PATH=/software/packages/htslib/1.4/lib
export LD_LIBRARY_PATH=/software/packages/htslib/1.4/lib

###
### Python 2.7.15 via module load
python \
/path/to/Platypus_0.8.1/Platypus.py \
callVariants \
--nCPU=4 \
--bamFiles=\
/path/to/Samp1.bam,\
/path/to/Samp2.bam \
--regions=/path/to/Capture_targets.txt \
--refFile=/path/to/human_g1k_v37.fasta \
--output=Platy_varCalls.vcf

The capture regions if provided, are to be in this format -

9:21970899-21971206
17:7577499-7577608
ADD REPLYlink written 11 weeks ago by Amitm2.1k
1

btw, the python code snippet you posted above, seems to be the Platypus.py file under src/python directory of the Platypus-master.zip file downloadable from the Github repo. If so, that is not the way to run Platypus. Please follow the instructions on the Github page. Btw, I realise that now this is available via Conda, which would be much easier way to go by.

ADD REPLYlink written 11 weeks ago by Amitm2.1k

Hi Amitm, thanks! I was albe to run it with Python2 as well now. It is not working eith python 3 and give me the error above.... also i could be able to download with conda but only with python2...

ADD REPLYlink written 11 weeks ago by User000440
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