Пример #1
0
 def __init__(self, model_file, bl_scaler=1.0, alphabet=('A', 'T','G','C')):
     self.model_file = model_file
     self.alphabet   = alphabet
     self.epsilon    = 10.0**-10 # A small value.
     self.model      = self.read_model(model_file)
     self.bl_scaler  = bl_scaler
     u.check_cmd('R')
Пример #2
0
 def __init__(self,
              model_file,
              bl_scaler=1.0,
              alphabet=('A', 'T', 'G', 'C')):
     self.model_file = model_file
     self.alphabet = alphabet
     self.epsilon = 10.0**-10  # A small value.
     self.model = self.read_model(model_file)
     self.bl_scaler = bl_scaler
     u.check_cmd('R')
Пример #3
0
 def __init__(self, run_file, read_length, insert_size, log, rts):
     self.fq_tmp = 'tmp'
     self.log = log
     self.run_file = run_file
     self.read_length = read_length
     self.insert_size = insert_size
     self.isize = insert_size - 2 * read_length
     self.sim_cmd = self._build_sim_cmd()
     self.rts = rts
     u.check_cmd('simLibrary')
     u.check_cmd('simNGS')
Пример #4
0
 def __init__(self, run_file, read_length, insert_size, log, rts):
     self.fq_tmp     = 'tmp'
     self.log        = log
     self.run_file   = run_file
     self.read_length= read_length
     self.insert_size= insert_size
     self.isize      = insert_size - 2 * read_length
     self.sim_cmd    = self._build_sim_cmd()
     self.rts        = rts
     u.check_cmd('simLibrary')
     u.check_cmd('simNGS')
Пример #5
0
 def __init__(self, fqs, kmer_length, min_ctgl, ins_len, max_div, rts, log, clean=False, asm_dir="assembly"):
     self.log        = log
     self.rts        = rts
     self.fqs        = fqs
     self.kmer_length= kmer_length
     self.min_ctgl   = min_ctgl
     self.ins_len    = ins_len
     self.max_div    = max_div
     self.clean      = clean
     self.asm_rts    = self.rts.subdir(asm_dir)
     self.asm_dir    = self.asm_rts.base
     u.check_cmd('velveth')
     u.check_cmd('velvetg')
Пример #6
0
    def plot(self, plotdir, partition, annotations, reco_info=None, cpath=None, no_mds_plots=False):
        if self.args.only_csv_plots:
            print '  --only-csv-plots not implemented for partition plots, so returning without plotting'
            return
        if not utils.check_cmd('R', options=['--slave', '--version'], return_bool=True):
            no_mds_plots = True
            print '  note: R does not seem to be installed, so skipping mds partition plots'
        print '  plotting partitions'
        sys.stdout.flush()
        start = time.time()

        fnames = []
        self.remove_failed_clusters(partition, annotations)
        sorted_clusters = sorted(partition, key=lambda c: len(c), reverse=True)
        fnames += self.make_shm_vs_cluster_size_plots(sorted_clusters, annotations, plotdir)
        if not no_mds_plots:
            fnames += self.make_mds_plots(sorted_clusters, annotations, plotdir, reco_info=reco_info, run_in_parallel=True) #, color_rule='wtf')
        # fnames += self.make_laplacian_spectra_plots(sorted_clusters, annotations, plotdir, cpath=cpath)
        # fnames += self.make_sfs_plots(sorted_clusters, annotations, plotdir)
        csfns = self.make_cluster_size_distribution(plotdir, partition)
        fnames[0] += csfns[0]

        if not self.args.only_csv_plots:
            self.plotting.make_html(plotdir, fnames=fnames, new_table_each_row=True, htmlfname=plotdir + '/overview.html', extra_links=[(subd, '%s/%s.html' % (plotdir, subd)) for subd in ['shm-vs-size', 'mds', 'laplacian-spectra']])  # , 'sfs

        print '    partition plotting time: %.1f sec' % (time.time()-start)
Пример #7
0
 def __init__(self,
              fqs,
              kmer_length,
              min_ctgl,
              ins_len,
              max_div,
              rts,
              log,
              clean=False,
              asm_dir="assembly"):
     self.log = log
     self.rts = rts
     self.fqs = fqs
     self.kmer_length = kmer_length
     self.min_ctgl = min_ctgl
     self.ins_len = ins_len
     self.max_div = max_div
     self.clean = clean
     self.asm_rts = self.rts.subdir(asm_dir)
     self.asm_dir = self.asm_rts.base
     u.check_cmd('velveth')
     u.check_cmd('velvetg')
Пример #8
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 def __init__(self, log, rts):
     u.check_cmd('muscle')
     self.log = log
     self.rts = rts.subdir('muscle')
Пример #9
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 def __init__(self, log, rts):
     self.log        = log
     self.rts        = rts
     u.check_cmd('exonerate')
Пример #10
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 def __init__(self, log, rts):
     self.log = log
     self.rts = rts
     u.check_cmd('exonerate')
Пример #11
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 def __init__(self, log, rts):
     u.check_cmd('muscle')
     self.log        = log
     self.rts        = rts.subdir('muscle')