Exemple #1
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 def __save_and_load_problem_npz(self, problem):
     '''Save and load a problem from NPZ file.'''
     out_file = tempfile.TemporaryFile()
     io.write_npz(problem, out_file)
     # Only needed here to simulate closing & reopening file; you will need to call 
     # out_file.close() on to prevent file locking in Windows
     out_file.seek(0)
     return io.read_npz(out_file)
Exemple #2
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 def __npz_to_plink(self, p, file_name):
     '''Convert p from npz to plink format using the file set specified by file_name.'''
     npz = file_name+'.npz'
     # Save test problem in plink format
     io.write_npz(p, npz)
     # Convert plink -> npz
     io.npz_to_plink(npz, file_name)
     # Load npz and check that the problem object didn't change
     p2 = io.read_plink(prefix=file_name)
     return p2
Exemple #3
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def __main(options):
    '''
    --------------------------------------------------
    Main program - accepts an options struct.
    --------------------------------------------------
    '''
    if options.debug: print 'Input options', options
    print 'Building phaser (stage = %d) ...' % (options.stage, )
    phaser = build_phasing_pipeline(options)

    if options.debug: print 'Reading data ...'
    problem = __load_problem(options)

    if options.debug: print 'Phasing ...'
    params = PhaseParam()
    params.update_from_struct(options)
    request = run_phasing_chain(phaser, problem, params)

    print ''
    request.stats.pprint()
    print ''

    if options.output is not None:
        if options.min_output:
            print 'Minimizing output size...'
            io.slim(problem)
        out_prefix, ext = os.path.splitext(options.output)
        if ext == '.npz':
            print 'Writing haplotype result to %s in NPZ format ...' % (
                options.output, )
            io.write_npz(problem, options.output)
            output_info = out_prefix + '.info.npz'
            print 'Writing problem info result to %s in NPZ format ...' % (
                output_info, )
            io.write_info_npz(problem.info, output_info)
        else:
            print 'Writing haplotype result to %s in PLINK format ...' % (
                options.output, )
            io.write_plink(problem, options.output, verbose=options.debug)
    return problem
Exemple #4
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def __main(options):
    '''
    --------------------------------------------------
    Main program - accepts an options struct.
    --------------------------------------------------
    '''
    if options.debug: print 'Input options', options
    print 'Building phaser (stage = %d) ...' % (options.stage,)
    phaser = build_phasing_pipeline(options)
    
    if options.debug: print 'Reading data ...'
    problem = __load_problem(options)

    if options.debug: print 'Phasing ...'
    params = PhaseParam()
    params.update_from_struct(options)
    request = run_phasing_chain(phaser, problem, params)
    
    print ''
    request.stats.pprint()
    print ''

    if options.output is not None:
        if options.min_output:
            print 'Minimizing output size...'
            io.slim(problem)
        out_prefix, ext = os.path.splitext(options.output)
        if ext == '.npz':
            print 'Writing haplotype result to %s in NPZ format ...' % (options.output,)
            io.write_npz(problem, options.output)
            output_info = out_prefix + '.info.npz'
            print 'Writing problem info result to %s in NPZ format ...' % (output_info,)
            io.write_info_npz(problem.info, output_info)
        else:
            print 'Writing haplotype result to %s in PLINK format ...' % (options.output,)
            io.write_plink(problem, options.output, verbose=options.debug)
    return problem
Exemple #5
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            util.run_command('%s --nonfounders --freq --out %s' % (plink_cmd_base, out_base_name))
            # Convert frequencies file that to a reference allele recoding
            # file (a file containing the list of SNPs and their minor allele letter)
            bu.frq_to_minor_file(out_base_name + '.frq', out_base_name + '.mnr') 

            # Then convert binary PLINK to a recoded 12-recoded TPED, where 1=minor allele for each SNP
            out_recoded = out_base_name + '.recoded'                 
            util.run_command('%s --transpose --recode12 --reference-allele %s.mnr --out %s' % \
                           (plink_cmd_base, out_base_name, out_recoded))

            # Reload the recoded problem
            for ext in ('nof', 'tped', 'tfam'):
                os.rename(out_recoded + '.' + ext, out_base_name + '.' + ext)
            genotype = io_genotype.read('plink', 'genotype', tped=out_base_name + '.tped', load_ids=False)
        else:
            genotype = problem.genotype
            
        # Write problem to file in our (npz)
        io.write_npz(problem, out_base_name + '.npz')
        # Write genotypes Gaixin formats; she uses those separate files
        io_genotype.write('gaixin', genotype, options.out_gxn + '.gxn',
                          sample_id=problem.pedigree.sample_id_genotyped)
             
        # Convert plink tped to bed; delete the tped set
        util.run_command('%s --make-bed --out %s' % (plink_cmd_base, out_base_name))
        for ext in ('nof', 'pdg.tfam', 'tped', 'tfam', 'info'):
            os.remove(out_base_name + '.' + ext)
    except:
        traceback.print_exc(file=sys.stdout)
        sys.exit(util.EXIT_FAILURE)