Failed to run haps_filters through multipop_selection_pipeline

[AhmedElfarargi]

I am testing the multipop_selection_pipeline with the test lactase data. After running the following command, I noticed that there's something went wrong with the selection_pipeline

multipop_selection_pipeline -p CEU_ids.txt -p YRI_ids.txt -i CEU_YRI_lactase.vcf --config-file defaults.cfg --a "--phased-vcf" -c 2

multi_population.log
selection_pipeline command = selection_pipeline -c 2 -i /SelectionPipelineTestData/lactase/CEU.vcf --population CEU --config-file defaults.cfg --phased-vcf
selection_pipeline failed to run selection_pipeline -c 2 -i /SelectionPipelineTestData/lactase/CEU.vcf --population CEU --config-file defaults.cfg --phased-vcf

CEU2_selection_pipeline.log
haps filter command = haps_filters --maf 0.01 --hwe 0.0001 --chi-sq --missing 0.99 --output CEU2_filtered.haps --haps CEU2vcf_to_haps.haps
haps filter failed to run haps_filters --maf 0.01 --hwe 0.0001 --chi-sq --missing 0.99 --output CEU2_filtered.haps --haps CEU2vcf_to_haps.haps
haps filter STDERR: Traceback (most recent call last):
haps filter STDERR: File "/bin/haps_filters", line 11, in
haps filter STDERR: load_entry_point('selectionTools==1.1.1', 'console_scripts', 'haps_filters')()
haps filter STDERR: File "/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/haps_filters.py", line 123
haps filter STDERR: filter_haps_file(args)
haps filter STDERR: File "/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/haps_filters.py", line 83,
haps filter STDERR: hardy_weinberg_asymptotic(countAB, countAA, countBB)
haps filter STDERR: File "/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/haps_filters.py", line 37,
haps filter STDERR: return stats.chisqprob(chi_sq_total, 1)
haps filter STDERR: AttributeError: 'module' object has no attribute 'chisqprob'

should I modify something within haps_filters.py file?

Thanks

[murraycadzow]

Hi,
It would appear that stats.chisqprob from SciPy has since been deprecated (https://docs.scipy.org/doc/scipy-0.19.1/reference/generated/scipy.stats.chisqprob.html).

A solution that might work is modifying the script to define the chisqprob function in the haps_filters.py

from scipy import stats
stats.chisqprob = lambda chisq, df: stats.chi2.sf(chisq, df)

Which I found here