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example_3.ini
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example_3.ini
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[Load Barcode Map]
_module = countess.plugins.csv
_class = LoadCsvPlugin
_version = 0.0.58
_hash = 52f1411c032e9f586e4fe4e288d0eb2e66a1fddc5693773cf67b1236d6a0d14e
_sort = 1 0
_position = 71 750
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
[FASTQ Load]
_module = countess.plugins.fastq
_class = LoadFastqPlugin
_version = 0.0.58
_hash = baf720adbe363ee25c43fda05ad94604ac7f990c693346be56dfc0d9354597a4
_sort = 0 0
_position = 71 250
files.0.filename = 'vampseq_1_1.fastq'
files.1.filename = 'vampseq_1_2.fastq'
files.2.filename = 'vampseq_2_1.fastq'
files.3.filename = 'vampseq_2_2.fastq'
files.4.filename = 'vampseq_3_1.fastq'
files.5.filename = 'vampseq_3_2.fastq'
files.6.filename = 'vampseq_4_1.fastq'
files.7.filename = 'vampseq_4_2.fastq'
min_avg_quality = 10.0
header_column = False
filename_column = True
group = True
[Variant Translator]
_module = countess.plugins.variant
_class = VariantPlugin
_version = 0.0.58
_hash = 74a7bb5fd36d3346669101453e6fc5fa1e9d4c1b50deb2959e77f467a0bb94b9
_sort = 1 0
_position = 214 750
_parent.0 = Load Barcode Map
column = 'sequence'
reference = 'ATGCTTTGTACGGGTGGTGCCCTGGCTTATCTATCTAGATCCGTCTCCGAGTCACGGTCGAATTTAGGTACTGCACTATCCTTTGAGGCGGGAAGGGCCACAAGGGCCGACCCTTGTCGGATAAAATTTGCTAAGAGGAAGGTCTAG'
output = 'variant'
max_mutations = 10
protein = 'protein'
offset = 0
max_protein = 10
drop = False
drop_columns = False
[Regex Tool]
_module = countess.plugins.regex
_class = RegexToolPlugin
_version = 0.0.58
_hash = a371d21451d0e0f0eeaff681d8d7d5c307d34ca3da420f879e28f893e49202ef
_sort = 0 0
_position = 214 250
_parent.0 = FASTQ Load
column = 'filename'
regex = 'vampseq_(\\d)_(\\d)\\.fastq'
output.0.name = 'bin'
output.0.datatype = 'integer'
output.1.name = 'rep'
output.1.datatype = 'integer'
drop_column = False
drop_unmatch = False
multi = False
[Join]
_module = countess.plugins.join
_class = JoinPlugin
_version = 0.0.58
_hash = 658c0d9a1078852fe6ebcc94b47c20c31295f235e53915bfe14baad566a28c74
_sort = 4 1
_position = 357 500
_parent.0 = Regex Tool
_parent.1 = Variant Translator
inputs.0.join_on = 'sequence'
inputs.0.required = True
inputs.0.drop = True
inputs.1.join_on = 'barcode'
inputs.1.required = True
inputs.1.drop = True
[Pivot on bin]
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.0.58
_hash = dd9f1f07fba44ed1efa3d0f647536e4b6bbf5ecb84058352eeba90ead0aaf5df
_sort = 1 0
_position = 500 500
_parent.0 = Join
columns.0._label = '"sequence_x"'
columns.0 = 'Drop'
columns.1._label = '"filename"'
columns.1 = 'Drop'
columns.2._label = '"count"'
columns.2 = 'Expand'
columns.3._label = '"bin"'
columns.3 = 'Pivot'
columns.4._label = '"rep"'
columns.4 = 'Index'
columns.5._label = '"sequence_y"'
columns.5 = 'Drop'
columns.6._label = '"variant"'
columns.6 = 'Drop'
columns.7._label = '"protein"'
columns.7 = 'Index'
[Calculate Score]
_module = countess.plugins.python
_class = PythonPlugin
_version = 0.0.58
_hash = 761f182b9392df4883e8fdaa9728044a930c745744474cd598308302450f56ec
_sort = 0 0
_position = 642 500
_parent.0 = Pivot on bin
code = 'score = (0.25 * count__bin_1 + 0.5 * count__bin_2 + 0.75 * count__bin_3 + count__bin_4) / (count__bin_1 + count__bin_2 + count__bin_3 + count__bin_4)\n\n'
dropna = False
[Pivot on Replicate]
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.0.58
_hash = dd9f1f07fba44ed1efa3d0f647536e4b6bbf5ecb84058352eeba90ead0aaf5df
_sort = 0 0
_position = 785 500
_parent.0 = Calculate Score
columns.0._label = '"rep"'
columns.0 = 'Pivot'
columns.1._label = '"protein"'
columns.1 = 'Index'
columns.2._label = '"count__bin_1"'
columns.2 = 'Drop'
columns.3._label = '"count__bin_2"'
columns.3 = 'Drop'
columns.4._label = '"count__bin_3"'
columns.4 = 'Drop'
columns.5._label = '"count__bin_4"'
columns.5 = 'Drop'
columns.6._label = '"score"'
columns.6 = 'Expand'
[Save Scores]
_module = countess.plugins.csv
_class = SaveCsvPlugin
_version = 0.0.58
_hash = 466b09d6a840cf0d7767324538760907fc8744e2e4f2a987e629c25782590bc4
_sort = 0 0
_position = 928 500
_parent.0 = Pivot on Replicate
header = True
filename = ''
delimiter = ','
quoting = False