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CreateSpecies.py
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CreateSpecies.py
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import SpeciesData as sd
"""Creates species as pickle is not working"""
def create_ferret_nasal(is_connectivity_index=False):
file = 'Ferret Nasal Wash & Lung NL09 WT_VAR Genotype Tables.xls'
sheet_number = 0
species_name = 'Ferret Nasal'
x_dimension_starts = [[1, 10, 19]] * 10
x_dimension_finishes = [[8, 17, 26]] * 10
y_dimension_starts = [[3] * 3, [26] * 3, [49] * 3, [72] * 3, [95] * 3, [118] * 3, [143] * 3, [166] * 3, [189] * 3,
[212] * 3]
y_dimension_finishes = [[23] * 3, [46] * 3, [69] * 3, [92] * 3, [115] * 3, [138] * 3, [163] * 3, [186] * 3,
[209] * 3,
[232] * 3]
individual_names = [f'F{number + 1}' for number in range(10)]
data_points = [['Day 1', 'Day 3', 'Day 5']] * 10
ferret_nasal_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points, split_point=6,
is_connectivity_index=is_connectivity_index)
return ferret_nasal_ds
def create_ferret_lung(is_connectivity_index=False):
file = 'Ferret Nasal Wash & Lung NL09 WT_VAR Genotype Tables.xls'
sheet_number = 1
species_name = 'Ferret Lung'
x_dimension_starts = [[1], [1], [10], [10], [19], [19], [28], [28], [1], [1], [10], [10], [19], [28]]
x_dimension_finishes = [[8], [8], [17], [17], [26], [26], [35], [35], [8], [8], [17], [17], [26], [35]]
y_dimension_starts = [[2], [25], [2], [25], [2], [25], [2], [25], [48], [71], [48], [71], [48], [48]]
y_dimension_finishes = [[22], [45], [22], [45], [22], [45], [22], [45], [68], [91], [68], [91], [68], [68]]
individual_names = ['F11', 'F12', 'F13', 'F14', 'F15', 'F16', 'F17', 'F18', 'F19', 'F20', 'F21', 'F22', 'F23',
'F24']
# individual_names = ['F12', 'F13', 'F14', 'F16', 'F17', 'F19', 'F20', 'F22', 'F23', 'F25', 'F27', 'F28', 'F30',
# 'F34']
data_points = [['Day 1']] * 2 + [['Day 2']] * 2 + [['Day 3']] * 2 + [['Day 4']] * 2 + [['Day 1']] * 2 + \
[['Day 2']] * 2 + [['Day 3']] + [['Day 4']]
ferret_lung_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points, split_point=8,
is_connectivity_index=is_connectivity_index)
return ferret_lung_ds
def create_ferret_lung_nasal(is_connectivity_index=False):
file = 'Ferret Nasal Turbinate & Lung NL09 WT_VAR Genotype Tables.xls'
sheet_number = 0
species_name = 'Ferret Lung and Nasal Turbinate'
x_dimension_starts = [[1, 1], [10, 10], [19, 19], [28, 28], [37, 37], [46, 46], [55, 55], [64, 64], [73, 73], [82, 82], [91, 91], [100, 100], [109, 109], [118, 118]]
x_dimension_finishes = [[8, 8], [17, 17], [26, 26], [35, 35], [44, 44], [53, 53], [62, 62], [71, 71], [80, 80], [89, 89], [98, 98], [107, 107], [116, 116], [125, 125]]
y_dimension_starts = [[2, 25]]*14
y_dimension_finishes = [[22, 45]]*14
individual_names = ['F11', 'F12', 'F13', 'F14', 'F15', 'F16', 'F17', 'F18', 'F19', 'F20', 'F21', 'F22', 'F23',
'F24']
# individual_names = ['F12', 'F13', 'F14', 'F16', 'F17', 'F19', 'F20', 'F22', 'F23', 'F25', 'F27', 'F28', 'F30',
# 'F34']
data_points = [['Lung', 'Nasal Turbinate']]*14
ferret_lung_nasal_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
split_point=8, is_connectivity_index=is_connectivity_index)
return ferret_lung_nasal_ds
def create_guinea_pig_nasal(is_connectivity_index=False):
file = 'Guinea Pig Nasal Wash Reassortment Genotype Tables.xls'
sheet_number = 0
species_name = 'Guinea Pig Nasal'
x_dimension_starts = [[1, 10, 19]] * 10
x_dimension_finishes = [[8, 17, 26]] * 10
y_dimension_starts = [[3] * 3, [26] * 3, [49] * 3, [72] * 3, [95] * 3, [118] * 3, [145] * 3, [167] * 3, [191] * 3,
[214] * 3]
y_dimension_finishes = [[23, 22, 23], [45, 46, 46], [69] * 3, [91, 92, 91], [115, 114, 113], [138, 137, 138],
[162, 162, 164], [187] * 3, [210, 211, 211], [233, 231, 234]]
individual_names = [f'GP{number + 1}' for number in range(10)]
data_points = [['Day 1', 'Day 2', 'Day 4']] * 6 + [['Day 1', 'Day 2', 'Day 3']] * 4
guinea_pig_nasal_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
split_point=6, is_connectivity_index=is_connectivity_index)
return guinea_pig_nasal_ds
def create_pig_lung_day3(is_connectivity_index=False):
file = 'Pig Lung Homogenate Genotype Tables.xls'
sheet_number = 0
species_name = 'Pig Lung Day 3'
x_dimension_starts = [[1] * 7, [10] * 7, [19] * 7]
x_dimension_finishes = [[8] * 7, [17] * 7, [26] * 7]
y_dimension_starts = [[2, 25, 48, 71, 94, 117, 140]] * 3
y_dimension_finishes = [[22, 45, 68, 91, 114, 137, 160]] * 3
individual_names = ['P1', 'P2', 'P3']
# individual_names = ['P79', 'P84', 'P73']
data_points = [['L.Apical', 'R.Apical', 'L.Cardiac', 'R.Cardiac', 'L.Diaphr', 'R.Diaphr', 'Intermed']] * 3
pig_lung_day3_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
is_spatial=True, is_connectivity_index=is_connectivity_index)
return pig_lung_day3_ds
def create_pig_lung_day5(is_connectivity_index=False):
file = 'Pig Lung Homogenate Genotype Tables.xls'
sheet_number = 1
species_name = 'Pig Lung Day 5'
x_dimension_starts = [[1] * 7, [10] * 7, [19] * 7]
x_dimension_finishes = [[8] * 7, [17] * 7, [26] * 7]
y_dimension_starts = [[2, 25, 94, 117, 48, 71, 140]] * 3
y_dimension_finishes = [[22, 45, 114, 137, 68, 91, 160]] * 3
individual_names = ['P4', 'P5', 'P6']
# individual_names = ['P55', 'P52', 'P76']
# data_points = [['L.Apical', 'R.Apical', 'L.Diaphr', 'R.Diaphr', 'L.Cardiac', 'R.Cardiac', 'Intermed']] * 3
data_points = [['L.Apical', 'R.Apical', 'L.Cardiac', 'R.Cardiac', 'L.Diaphr', 'R.Diaphr', 'Intermed']] * 3
pig_lung_day5_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
is_spatial=True, is_connectivity_index=is_connectivity_index)
return pig_lung_day5_ds
def create_pig_nasal(is_connectivity_index=False):
file = 'Pig Nasal Swab Genotype Tables.xls'
sheet_number = 0
species_name = 'Pig Nasal'
x_dimension_starts = [[1, 10, 19]] * 6
x_dimension_finishes = [[8, 17, 26]] * 6
y_dimension_starts = [[25] * 3, [2] * 3, [71] * 3, [48] * 3, [94] * 3, [117] * 3]
y_dimension_finishes = [[45] * 3, [22] * 3, [91] * 3, [68] * 3, [114] * 3, [137, 137, 135]]
individual_names = ['P4', 'P5', 'P6', 'P7', 'P8', 'P9']
# individual_names = ['P55', 'P52', 'P76', 'P66', 'P88', 'P89']
data_points = [['Day 1', 'Day 3', 'Day 5']] * 6
pig_nasal_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
is_connectivity_index=is_connectivity_index)
return pig_nasal_ds
def create_pig_lung_nasal_day5(is_connectivity_index=False):
file = 'Pig Lung Homogenate Genotype Tables.xls'
sheet_number = 1
species_name = 'Pig Lung and Nasal Day 5'
x_dimension_starts = [[1] * 8, [10] * 8, [19] * 8]
x_dimension_finishes = [[8] * 8, [17] * 8, [26] * 8]
y_dimension_starts = [[2, 25, 94, 117, 48, 71, 140, 163]] * 3
y_dimension_finishes = [[22, 45, 114, 137, 68, 91, 160, 183]] * 3
individual_names = ['P4', 'P5', 'P6']
# individual_names = ['P55', 'P52', 'P76']
# data_points = [['L.Apical', 'R.Apical', 'L.Diaphr', 'R.Diaphr', 'L.Cardiac', 'R.Cardiac', 'Intermed', 'Nasal']] * 3
data_points = [['L.Apical', 'R.Apical', 'L.Cardiac', 'R.Cardiac', 'L.Diaphr', 'R.Diaphr', 'Intermed', 'Nasal']] * 3
pig_lung_day5_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
is_spatial=True, is_connectivity_index=is_connectivity_index)
return pig_lung_day5_ds
def create_quail_tracheal(is_connectivity_index=False):
file = 'Quail Tracheal Swab Genotype Tables.xls'
sheet_number = 0
species_name = 'Quail Tracheal'
x_dimension_starts = [[1, 10, 19]] * 3 + [[1, 10]] + [[1, 10, 19]] * 6
x_dimension_finishes = [[8, 17, 26]] * 3 + [[8, 17]] + [[8, 17, 26]] * 6
y_dimension_starts = [[3] * 3, [26] * 3, [49] * 3, [72] * 2, [95] * 3, [118] * 3, [141] * 3, [164] * 3, [187] * 3,
[209] * 3]
y_dimension_finishes = [[23, 22, 23], [45, 45, 46], [69, 69, 68], [92] * 2, [115, 112, 114], [138] * 3, [161] * 3,
[184] * 3, [205, 205, 206], [229, 230, 230]]
individual_names = ['Q19', 'Q20', 'Q21', 'Q22', 'Q23', 'Q24', 'Q41', 'Q42', 'Q44', 'Q45']
data_points = [['Day 1', 'Day 3', 'Day 5']] * 3 + [['Day 1', 'Day 3']] + [['Day 1', 'Day 3', 'Day 5']] * 6
quail_tracheal_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes,
y_dimension_starts, y_dimension_finishes, individual_names, data_points,
split_point=6, is_connectivity_index=is_connectivity_index)
return quail_tracheal_ds
def create_guinea_pig_verify():
"""Creates guinea pig species from previous study to verify code is working"""
file = 'GP Reassortment_H3N8_H4N6.xls'
sheet_number = 0
species_name = 'Guinea Pig'
x_dimension_starts = [[1, 10, 19]] * 8
x_dimension_finishes = [[8, 17, 26]] * 8
y_dimension_starts = [[2] * 3, [25] * 3, [48] * 3, [71] * 3, [94] * 3, [117] * 3, [140] * 3, [163] * 3]
y_dimension_finishes = [[22] * 3, [45] * 3, [68] * 3, [91] * 3, [114] * 3, [137] * 3, [160] * 3, [183] * 3]
individual_names = [f'GP#{number + 1}' for number in range(8)]
data_points = [['Day 1', 'Day 2', 'Day 3']] * 8
GP_ds = sd.Species(file, sheet_number, species_name, x_dimension_starts, x_dimension_finishes, y_dimension_starts,
y_dimension_finishes, individual_names, data_points)
return GP_ds