Getting basic info out of a PMO

Code

from pmotools.pmo_utils.PMOExtractor import PMOExtractor
from pmotools.pmo_utils.PMOReader import PMOReader
from pmotools.utils.small_utils import Utils


pmo = PMOReader.read_in_pmo("../format/moz2018_PMO.json.gz")

Getting sample counts per target

Code

# get counts of the samples per target
counts_df = PMOExtractor.count_samples_per_target(pmo)

print(counts_df)

   tar_amp_bioinformatics_info_id target_id sample_number
0         Mozambique2018-SeekDeep        t1           119
0         Mozambique2018-SeekDeep       t10           117
0         Mozambique2018-SeekDeep      t100           124
0         Mozambique2018-SeekDeep       t11           120
0         Mozambique2018-SeekDeep       t12           119
..                            ...       ...           ...
0         Mozambique2018-SeekDeep       t96           119
0         Mozambique2018-SeekDeep       t97           122
0         Mozambique2018-SeekDeep       t98           122
0         Mozambique2018-SeekDeep       t99           120
0         Mozambique2018-SeekDeep       t76            32

[100 rows x 3 columns]

Getting target counts per sample

Code

# get counts of the samples per target
target_counts_df = PMOExtractor.count_targets_per_sample(pmo)
print(target_counts_df)

   tar_amp_bioinformatics_info_id experiment_sample_id target_number
0         Mozambique2018-SeekDeep           8025874217            99
0         Mozambique2018-SeekDeep           8025874231            99
0         Mozambique2018-SeekDeep           8025874234            97
0         Mozambique2018-SeekDeep           8025874237            99
0         Mozambique2018-SeekDeep           8025874250            98
..                            ...                  ...           ...
0         Mozambique2018-SeekDeep           SS1-10K-C1            98
0         Mozambique2018-SeekDeep           SS2-10K-C1            98
0         Mozambique2018-SeekDeep           SS3-10K-C1            98
0         Mozambique2018-SeekDeep           SS4-10K-C1            99
0         Mozambique2018-SeekDeep           SS5-10K-C1            97

[124 rows x 3 columns]