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example_2.ini
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example_2.ini
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[CSV Load Sequences]
_module = countess.plugins.csv
_class = LoadCsvPlugin
_version = 0.0.58
_hash = e7904a09ddab616835efca358e5668c31330e7ba3cc96042cec40024827ebdc0
_sort = 1 0
_position = 71 250
files.0.filename = 'sequences_1.csv'
files.1.filename = 'sequences_2.csv'
delimiter = ','
quoting = 'None'
comment = 'None'
header = True
filename_column = ''
columns.0.name = 'barcode'
columns.0.type = 'string'
columns.0.index = False
columns.1.name = 'time'
columns.1.type = 'integer'
columns.1.index = False
[CSV Load Barcodes]
_module = countess.plugins.csv
_class = LoadCsvPlugin
_version = 0.0.58
_hash = 52f1411c032e9f586e4fe4e288d0eb2e66a1fddc5693773cf67b1236d6a0d14e
_sort = 0 0
_position = 213 750
files.0.filename = 'barcodes.csv'
delimiter = ','
quoting = 'None'
comment = 'None'
header = True
filename_column = ''
columns.0.name = 'barcode'
columns.0.type = 'string'
columns.0.index = False
columns.1.name = 'sequence'
columns.1.type = 'string'
columns.1.index = False
[Group By Barcode]
_module = countess.plugins.group_by
_class = GroupByPlugin
_version = 0.0.58
_hash = b8c2f5475e1bd8398634ff0a6f7b130b3f9c879fb10579f0c2f81f30f1f01508
_sort = 0 0
_position = 213 250
_parent.0 = CSV Load Sequences
columns.0._label = '"barcode"'
columns.0.index = True
columns.0.count = False
columns.0.min = False
columns.0.max = False
columns.0.sum = False
columns.0.mean = False
columns.1._label = '"time"'
columns.1.index = True
columns.1.count = False
columns.1.min = False
columns.1.max = False
columns.1.sum = False
columns.1.mean = False
join = False
[Join on Barcode]
_module = countess.plugins.join
_class = JoinPlugin
_version = 0.0.58
_hash = 03767a6446eda58e7b229f41d23f2708bee23dd5515e46a50c6e85d3cfc67cfa
_sort = 3 0
_position = 357 500
_parent.0 = Group By Barcode
_parent.1 = CSV Load Barcodes
inputs.0.join_on = 'barcode'
inputs.0.required = True
inputs.0.drop = False
inputs.1.join_on = 'barcode'
inputs.1.required = True
inputs.1.drop = False
[Variant Translator]
_module = countess.plugins.variant
_class = VariantPlugin
_version = 0.0.58
_hash = 74a7bb5fd36d3346669101453e6fc5fa1e9d4c1b50deb2959e77f467a0bb94b9
_sort = 0 0
_position = 500 500
_parent.0 = Join on Barcode
column = 'sequence'
reference = 'ATGCTTTGTACGGGTGGTGCCCTGGCTTATCTATCTAGATCCGTCTCCGAGTCACGGTCGAATTTAGGTACTGCACTATCCTTTGAGGCGGGAAGGGCCACAAGGGCCGACCCTTGTCGGATAAAATTTGCTAAGAGGAAGGTCTAG'
output = 'variant'
max_mutations = 10
protein = 'protein'
offset = 0
max_protein = 10
drop = False
drop_columns = False
[Pivot by Time (Protein)]
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.0.58
_hash = dd9f1f07fba44ed1efa3d0f647536e4b6bbf5ecb84058352eeba90ead0aaf5df
_sort = 0 0
_position = 642 750
_parent.0 = Variant Translator
columns.0._label = '"barcode"'
columns.0 = 'Drop'
columns.1._label = '"time"'
columns.1 = 'Pivot'
columns.2._label = '"count"'
columns.2 = 'Expand'
columns.3._label = '"sequence"'
columns.3 = 'Drop'
columns.4._label = '"variant"'
columns.4 = 'Drop'
columns.5._label = '"protein"'
columns.5 = 'Index'
[Calculate Score (Protein)]
_module = countess.plugins.python
_class = PythonPlugin
_version = 0.0.58
_hash = 761f182b9392df4883e8fdaa9728044a930c745744474cd598308302450f56ec
_sort = 0 0
_position = 785 750
_parent.0 = Pivot by Time (Protein)
code = 'score = (\n count__time_2 / count__time_1\n if count__time_1 else None\n)\n\n'
dropna = False
[CSV Save (Protein)]
_module = countess.plugins.csv
_class = SaveCsvPlugin
_version = 0.0.58
_hash = 466b09d6a840cf0d7767324538760907fc8744e2e4f2a987e629c25782590bc4
_sort = 0 0
_position = 927 750
_parent.0 = Calculate Score (Protein)
header = True
filename = 'output_protein.csv'
delimiter = ','
quoting = False
[Pivot by Time (DNA)]
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.0.58
_hash = dd9f1f07fba44ed1efa3d0f647536e4b6bbf5ecb84058352eeba90ead0aaf5df
_sort = 0 0
_position = 642 250
_parent.0 = Variant Translator
columns.0._label = '"barcode"'
columns.0 = 'Drop'
columns.1._label = '"time"'
columns.1 = 'Pivot'
columns.2._label = '"count"'
columns.2 = 'Expand'
columns.3._label = '"sequence"'
columns.3 = 'Drop'
columns.4._label = '"variant"'
columns.4 = 'Index'
columns.5._label = '"protein"'
columns.5 = 'Drop'
[Calculate Score (DNA)]
_module = countess.plugins.python
_class = PythonPlugin
_version = 0.0.58
_hash = 761f182b9392df4883e8fdaa9728044a930c745744474cd598308302450f56ec
_sort = 0 0
_position = 785 250
_parent.0 = Pivot by Time (DNA)
code = 'score = (\n count__time_2 / count__time_1\n if count__time_1 else None\n)\n\n'
dropna = False
[CSV Save (DNA)]
_module = countess.plugins.csv
_class = SaveCsvPlugin
_version = 0.0.58
_hash = 466b09d6a840cf0d7767324538760907fc8744e2e4f2a987e629c25782590bc4
_sort = 0 0
_position = 927 250
_parent.0 = Calculate Score (DNA)
header = True
filename = 'output_dna.csv'
delimiter = ','
quoting = False