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| #!/usr/bin/env python | |
| ################################################# | |
| # importing the wrapper | |
| ################################################# | |
| import sys,os | |
| #add path for isomut_wrappers.py | |
| # if not running it from the isomut directory | |
| # change os.getcwd for the path to it | |
| sys.path.append(os.getcwd()+'/src') | |
| #load the parallel wrapper function | |
| from isomut_wrappers import run_isomut | |
| #add path for isomut, if its in the path comment/delete this line | |
| # if not running it from the isomut directory | |
| # change os.getcwd for the path to it | |
| os.environ["PATH"] += os.pathsep + os.getcwd() +'/src' | |
| ################################################# | |
| # defining administrative parameters | |
| ################################################# | |
| #using parameter dictionary, beacause there are awful lot of parameters | |
| params=dict() | |
| #minimum number of blocks to run | |
| # usually there will be 10-20 more blocks | |
| params['n_min_block']=200 | |
| #number of concurrent processes to run | |
| params['n_conc_blocks']=4 | |
| #genome | |
| params['ref_fasta']="/home/ribli/input/index/gallus/Gallus_gallus.Galgal4.74.dna.toplevel.fa" | |
| #input dir output dir | |
| params['input_dir']='/nagyvinyok/adat86/sotejedlik/ribli/dt40/test_bams/' | |
| params['output_dir']='isomut_test_output/' | |
| #the bam files used | |
| params['bam_filenames']=['DS014.bam', 'DS051.bam', 'DS052.bam', 'DS053.bam', 'DS054.bam', 'DS055.bam', | |
| 'DS056.bam', 'DS057.bam', 'DS058.bam', 'DS101.bam', 'DS102.bam', 'DS103.bam'] | |
| #limit chromosomes (for references with many scaffolds) | |
| # just comment/delete this line if you want to analyze all contigs in the ref genome | |
| params['chromosomes']=map(str,range(1,29))+ ['32','W','Z','MT'] | |
| ################################################# | |
| # defining mutation calling parameters | |
| # default values here ... | |
| ################################################# | |
| params['min_sample_freq']=0.21 | |
| params['min_other_ref_freq']=0.93 | |
| params['cov_limit']=5 | |
| params['base_quality_limit']=30 | |
| params['min_gap_dist_snv']=0 | |
| params['min_gap_dist_indel']=20 | |
| ################################################# | |
| # and finally run it | |
| ################################################# | |
| run_isomut(params) |