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jon-xu / scSplit

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
MIT License
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syntax error in scSplit count #5

Closed jagregory17 closed 5 years ago

jagregory17 commented 5 years ago

Hello,

I'm a running python 3.7 and created an environment with the appropriate modules so it can later be called when submitting a job to the cluster for scSplit count. I'm having trouble building the account matrices though.

packages in environment at /PATHtoENV/conda/scSplit-env:

blas 1.0 mkl
certifi 2016.2.28 py27_0
docutils 0.15.2 py27_0 conda-forge libgfortran 3.0.0 1
mkl 2017.0.3 0
numpy 1.13.1 py27_0
openssl 1.0.2l 0
pandas 0.20.3 py27_0
pip 9.0.1 py27_1
pysam 0.6 py27_0
python 2.7.13 0
python-dateutil 2.6.1 py27_0
pytz 2017.2 py27_0
pyvcf 0.6.8 py27_1000 conda-forge readline 6.2 2
scikit-learn 0.19.0 np113py27_0
scipy 0.19.1 np113py27_0
setuptools 36.4.0 py27_1
six 1.10.0 py27_0
sqlite 3.13.0 0
statistics 1.0.3.5 py_1002 conda-forge tk 8.5.18 0
wheel 0.29.0 py27_0
zlib 1.2.11 0

the following command throws a syntax error:

python /PathToscript/scSplit/scSplit count \ -v $mixedvcf \ -i $filteredbam \ -b $barcodes \ -r ${BASEDIR}/ref_filtered.csv \ -a ${BASEDIR}/alt_filtered.csv

I'm getting the following error:

File "/pathtoscript/github/scSplit/scSplit", line 104 rows, cols = [range(base_mtx.shape[0])], [range(base_mtx.shape[1])] ^ SyntaxError: invalid syntax

The comments immediately preceding this command refer to the barcodes:

find barcodes for state initialization, using subsetting/PCA/K-mean

as far as I can tell the barcodes.tsv is fine and the path is correct. Any suggestions?

jon-xu commented 5 years ago

Hi Jagregory17,

Are you sure you are running on Python 3.7? - It seems like a syntax error from Python 2.7.

Would you mind checking again and letting me know?

Cheers, Jon

jagregory17 commented 5 years ago

I think you are right. despite having loaded python 3.7, it was using version 2.7 when checked the version of python from within the bash script. I think i must have created the conda environment with the default python version on the cluster, and so when i activated that environment it loaded python 2.7. Thanks so much!

jon-xu commented 5 years ago

Great to know! Feel free if there is any other issues.

I'll close this one. Cheers, Jon