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Fixed parameter typo, default value, and TypeError #13

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Fixed parameter typo, default value, and TypeError #13

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4 changes: 2 additions & 2 deletions src/SGVF_cmd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ def _addargs(parser):
parser.add_argument('input_glob', help = 'A glob string that includes all the files processed with the PerFile_cmd')
parser.add_argument('output_dsgv', help = 'Output path for the deletion-sgv dataframe. By default a pickled pandas dataframe')
parser.add_argument('output_vsgv', help = 'Output path for the variable-sgv dataframe. By default a pickled pandas dataframe')
parser.add_argument('--x_coverage', help = 'The desired coverage across the genome in units of 100bp reads. This parameter is used to determine bin size: bin_size = rate_param/x_coverage (Default = 0.1)', type=float, default = 0.1)
parser.add_argument('--x_coverage', help = 'The desired coverage across the genome in units of 100bp reads. This parameter is used to determine bin size: bin_size = rate_param/x_coverage (Default = 0.1)', type=float, default = 0.01)
parser.add_argument('--rate_param', help = 'The lower limit for the median number of reads per genomic bin. Genomes with coverage lower than rate_param will be discarded from the analysis (Default = 10)', type = int, default = 10)
parser.add_argument('--byorig', help = 'Calculate SGVs according to the regions published by Zeevi et al, XXX, 201Y.', action = 'store_true')
parser.add_argument('--min_samp_cutoff', help = 'Minimum number of samples in which a microbe exists with sufficient coverage to be considered in the analysis (Default=75)', type=int, default = 75)
Expand All @@ -36,7 +36,7 @@ def _load_ujsn(fname):
_addargs(parser)
args = parser.parse_args()
samp_to_map = {splitext(basename(f))[0]: _load_ujsn(f) for f in glob(args.input_glob)}
if args.byother:
if args.byorig:
vsgv, dsgv = calculate_by_other(join(split(realpath(__file__))[0], '../DataFiles/orig_dsgv.df'),
join(split(realpath(__file__))[0], '../DataFiles/orig_vsgv.df'),
join(split(realpath(__file__))[0], '../DataFiles/orig_frames'),
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4 changes: 2 additions & 2 deletions src/SGVFinder.py
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Expand Up @@ -29,10 +29,10 @@ def get_sample_map(delta_fname, x_coverage, average_read_length, rate_param):
for dest_id, pos1, pos2, used_koef, _ in mapngs:
if dest_id not in bacid_maps:
bacid_maps[dest_id] = np.zeros(int(lengthdb[dest_id] / bin_size) + 1)
ind1 = int((pos1 + (average_read_length / 2)) / bin_size)
ind1 = int((int(pos1) + (int(average_read_length) / 2)) / bin_size)
if pos2 >= 0:
used_koef = used_koef / 2.0
ind2 = int((pos2 + (average_read_length / 2)) / bin_size)
ind2 = int((int(pos2) + (int(average_read_length) / 2)) / bin_size)
bacid_maps[dest_id][ind2] += used_koef
bacid_maps[dest_id][ind1] += used_koef
return {dest_id:cov_map for dest_id, cov_map in bacid_maps.iteritems()\
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