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Copy pathchr27_mystery_run_for_range_rho.py
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chr27_mystery_run_for_range_rho.py
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import subprocess
rho = [0.000005, 0.00001, 0.00005, 0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1, 0.5]
for ix, rho_val in enumerate(rho):
out1 = 'chr27_haplotypes%s_subset2_now' % ix
out2 = 'chr27_haplotypes%s_subset2_w' % ix
call1 = '/mnt/lustre/home/sonal.singhal1/bin/shapeit_v2r790/shapeit -assemble --input-vcf /mnt/gluster/home/sonal.singhal1/ZF/after_vqsr/by_chr/unrel_vcf/gatk.ug.unrel_zf.chr27.coverage.filtered.recoded_biallelicSNPs.nomendel.vcf_subset2.gz --input-pir /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/chr27_PIRlist -O /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s -L /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s.log --thread 8 --output-graph /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s.graph --rho %s' % (out1, out1, out1, rho_val)
call2 = '/mnt/lustre/home/sonal.singhal1/bin/shapeit_v2r790/shapeit -assemble --input-vcf /mnt/gluster/home/sonal.singhal1/ZF/after_vqsr/by_chr/unrel_vcf/gatk.ug.unrel_zf.chr27.coverage.filtered.recoded_biallelicSNPs.nomendel.vcf.gz --input-pir /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/chr27_PIRlist -O /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s -L /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s.log --thread 8 --output-graph /mnt/gluster/home/sonal.singhal1/ZF/phasing/PIR_approach/%s.graph --rho %s --window 0.5' % (out2, out2, out2, rho_val)
subprocess.call('echo \"%s\" | qsub -l h_vmem=2g -cwd -V -j y -N %s' % (call1, out1), shell=True)
subprocess.call('echo \"%s\" | qsub -l h_vmem=2g -cwd -V -j y -N %s' % (call2, out2), shell=True)