20260217_final_TSC2_lib2.ini

[fastq_load]
_uuid = 8c50320c1e10dbcd837e725ab009f5ff
_module = countess.plugins.fastq
_class = LoadFastqPlugin
_version = 0.1.16
_hash = 581df0895c9ae50c09acef102d12e2422ac4a5e82d990ca34916be60f6a87c7a
_sort = 1 1
_position = 51 198
files.0.filename = 'TSC2_fastqs/L2R1B1.fastq'
files.1.filename = 'TSC2_fastqs/L2R1B2.fastq'
files.2.filename = 'TSC2_fastqs/L2R1B3.fastq'
files.3.filename = 'TSC2_fastqs/L2R1B4.fastq'
files.4.filename = 'TSC2_fastqs/L2R2B1.fastq'
files.5.filename = 'TSC2_fastqs/L2R2B2.fastq'
files.6.filename = 'TSC2_fastqs/L2R2B3.fastq'
files.7.filename = 'TSC2_fastqs/L2R2B4.fastq'
files.8.filename = 'TSC2_fastqs/L2R3B1.fastq'
files.9.filename = 'TSC2_fastqs/L2R3B2.fastq'
files.10.filename = 'TSC2_fastqs/L2R3B3.fastq'
files.11.filename = 'TSC2_fastqs/L2R3B4.fastq'
filename_column = True
min_avg_quality = 10.0
header_column = False
group = True

[barcode_map_load]
_uuid = a2c2656a29c19005d6e3734095f671cd
_module = countess.plugins.csv
_class = LoadCsvPlugin
_version = 0.1.16
_hash = 609bbffd4bf37750bc97e1d27447bc8a145ddf47eeaac3c2405e65342b34c120
_sort = 0 0
_position = 50 750
files.0.filename = 'TSC2_lib2_map_revised.csv'
filename_column = False
delimiter = ','
header = True
columns.0.name = 'barcodes'
columns.0.type = 'STRING'
columns.1.name = 'aaChanges'
columns.1.type = 'STRING'

[drop filename column]
_uuid = 020331a645b3813707d628d0dc85a324
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = 487d7b7ed39766acbff66ee0628efdc17f25ed1965af9d7f0294145d6573b49f
_sort = 1 1
_position = 159 88
_parent.0 = fastq_load
code = 'filename = None\n\n'

[Count Threshold]
_uuid = 7f786def8309651afbe4359cf6935725
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = f08d312ef5c9367eebb379cf96e2bd2bfc2bb090ce720bea2e4bed0b05efa6f0
_sort = 0 0
_position = 253 276
_parent.0 = drop filename column
code = '__filter = count>2\n\n'

[Variant Converter]
_uuid = 9659c105a2b29dc9428899f299daa68b
_module = countess.plugins.variant
_class = VariantConverter
_version = 0.1.16
_hash = 021f82f49187fa452669ea73aec5448173d18e9de3bdb32965534652397c9f46
_sort = 1 0
_position = 150 750
_parent.0 = barcode_map_load
variant_col = 'aaChanges'
variant_out = 'variant'
prefix_aa = 'ENSP00000219476.3'
prefix_nt = ''
offset = 1511

[drop count column]
_uuid = 7824afccec0057d5f857061c7edef3fe
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = dd32f4407df68d7e23a14422e03ed2fc5171ceeade2ff84dc138fed792357746
_sort = 0 0
_position = 50 535
_parent.0 = Count Threshold
code = 'count=None\n\n'

[Thresholded barcode counts]
_uuid = 708061bc45ef3ca245a27f8e61a5ac17
_module = countess.plugins.join
_class = JoinPlugin
_version = 0.1.16
_hash = 9365980308790ef3ce735c62d657e37f51bf3fa85488005edfb64541c3573488
_sort = 0 0
_position = 148 600
_parent.0 = fastq_load
_parent.1 = drop count column
inputs.0.join_on = 'sequence'
inputs.0.join_2 = '— NONE —'
inputs.0.join_3 = '— NONE —'
inputs.0.required = False
inputs.0.drop = False
inputs.1.join_on = 'sequence'
inputs.1.join_2 = '— NONE —'
inputs.1.join_3 = '— NONE —'
inputs.1.required = True
inputs.1.drop = True

[parse_filename]
_uuid = 7b4b06d42fd92f137b71a39c284b8fd9
_module = countess.plugins.regex
_class = RegexToolPlugin
_version = 0.1.16
_hash = 640dee47cd10e0322eaecd3689b4d42b6b6a4c50ac24a4a214d119fc9f63c310
_sort = 0 1
_position = 250 624
_parent.0 = Thresholded barcode counts
column = 'filename'
regex = ' ?L2R(\\d+)B(\\d+)?'
output.0.name = 'replicate'
output.0.datatype = 'INTEGER'
output.1.name = 'bin'
output.1.datatype = 'INTEGER'
drop_column = True
drop_unmatch = False

[join_on_barcode]
_uuid = 6b793355bc9e58633bdea888e39f0b50
_module = countess.plugins.join
_class = JoinPlugin
_version = 0.1.16
_hash = cbef6a2bf0b78601e6a56a2008eb5f626818f8967879f2a7de0587bc7c946a14
_sort = 2 1
_position = 350 750
_parent.0 = parse_filename
_parent.1 = Variant Converter
inputs.0.join_on = 'sequence'
inputs.0.join_2 = '— NONE —'
inputs.0.join_3 = '— NONE —'
inputs.0.required = True
inputs.0.drop = True
inputs.1.join_on = 'barcodes'
inputs.1.join_2 = '— NONE —'
inputs.1.join_3 = '— NONE —'
inputs.1.required = True
inputs.1.drop = True

[pivot_bins]
_uuid = df3c55d9b2f6a89390fbc7d684691fe5
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.1.16
_hash = e8258e54cb399e645b10e3124911d84114f21fa9f6184756fd646c59c50b9add
_sort = 0 0
_position = 447 750
_parent.0 = join_on_barcode
columns.0._label = 'count'
columns.0 = 'Expand'
columns.1._label = 'replicate'
columns.1 = 'Index'
columns.2._label = 'bin'
columns.2 = 'Pivot'
columns.3._label = 'aaChanges'
columns.3 = 'Index'
columns.4._label = 'variant'
columns.4 = 'Index'
aggfunc = 'sum'
default_0 = True
short_names = True

[VAMP-seq Scoring]
_uuid = 63e185eb303e6a1d1e337808e9f52a9d
_module = countess.plugins.vampseq
_class = VampSeqScorePlugin
_version = 0.1.16
_hash = a4a8421b2e5b19de7ea417fc2529d3c7b996d0094d419c988cd18c4a2b6d3e8d
_sort = 1 1
_position = 447 240
_parent.0 = pivot_bins
columns.0._label = 'replicate'
columns.0.weight = None
columns.1._label = 'count_1'
columns.1.weight = 0.25
columns.2._label = 'count_2'
columns.2.weight = 0.5
columns.3._label = 'count_3'
columns.3.weight = 0.75
columns.4._label = 'count_4'
columns.4.weight = 1.0
group_by.0._label = 'replicate'
group_by.0 = True
group_by.1._label = 'aaChanges'
group_by.1 = False
group_by.2._label = 'variant'
group_by.2 = False
group_by.3._label = 'count_1'
group_by.3 = False
group_by.4._label = 'count_2'
group_by.4 = False
group_by.5._label = 'count_3'
group_by.5 = False
group_by.6._label = 'count_4'
group_by.6 = False

[Classify]
_uuid = d621cb5e0bb8063b440d8ff7ee743348
_module = countess.plugins.variant
_class = VariantClassifier
_version = 0.1.16
_hash = a447a85eecc171f2a5c8ba8fb3bfd474e1de0a8934dd4713c91296c95283ce65
_sort = 6 0
_position = 508 221
_parent.0 = VAMP-seq Scoring
variant_col = 'aaChanges'

[Ranking]
_uuid = 3a0989617bb069c4f6faa21ff730a289
_module = countess.plugins.ranking
_class = RankingPlugin
_version = 0.1.16
_hash = f8970811d3d663e8fb8e4bd3e44327e76041154852079f134f032fc7a22f36d5
_sort = 8 1
_position = 556 221
_parent.0 = Classify
order_by.0 = 'score'
partition.0 = 'replicate'
partition.1 = 'aaChanges_type'

[label bottom 5 percent of missense]
_uuid = f43ce446c6262aa6c6a363f90e2a7040
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = cb9f5a878446d62135c2497dc9f4a352c4bbe8c2f62e7a2de201992125862c61
_sort = 0 0
_position = 521 436
_parent.0 = Ranking
code = 'dumb_solution =aaChanges_type == "M" and rank <= 0.05\n\n'

[convert boolean to string]
_uuid = 37c04eeb31c68538229f8d5867e7498a
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = 886d65339c016ac81b7854e0e253685030a881b5155303362bb733f625948800
_sort = 0 0
_position = 600 490
_parent.0 = label bottom 5 percent of missense
code = 'dumb_solution_string = "TRUE" if dumb_solution else "FALSE"\n\n'

[Scale Scores]
_uuid = 0241d1d2ccfd4e58918225d430e2bc65
_module = countess.plugins.score_scale
_class = ScoreScalingPlugin
_version = 0.1.16
_hash = db4cee8cb3b954146fb04c4d3151ad07cef96fad04fecd5151679e2aa8986edc
_sort = 0 0
_position = 650 500
_parent.0 = convert boolean to string
score_col = 'score'
scaled_col = 'abundance'
classifiers.0.agg = 'Median'
classifiers.0.col = 'dumb_solution_string'
classifiers.0.op = 'Matches'
classifiers.0.st = 'TRUE'
classifiers.1.agg = 'Median'
classifiers.1.col = 'aaChanges_type'
classifiers.1.op = 'Matches'
classifiers.1.st = 'W'

[pivot_replicates]
_uuid = 4573f843591167b99b9a1b1d9729e3f7
_module = countess.plugins.pivot
_class = PivotPlugin
_version = 0.1.16
_hash = 0f7625a1c5cd47aaaf08b82513f517b1823b4a6d27631e5f1f2a21d17ed61465
_sort = 0 1
_position = 750 250
_parent.0 = Scale Scores
columns.0._label = 'replicate'
columns.0 = 'Pivot'
columns.1._label = 'aaChanges'
columns.1 = 'Index'
columns.2._label = 'variant'
columns.2 = 'Index'
columns.3._label = 'count_1'
columns.3 = 'Drop'
columns.4._label = 'count_2'
columns.4 = 'Drop'
columns.5._label = 'count_3'
columns.5 = 'Drop'
columns.6._label = 'count_4'
columns.6 = 'Drop'
columns.7._label = 'score'
columns.7 = 'Drop'
columns.8._label = 'aaChanges_type'
columns.8 = 'Index'
columns.9._label = 'rank'
columns.9 = 'Drop'
columns.10._label = 'dumb_solution'
columns.10 = 'Drop'
columns.11._label = 'dumb_solution_string'
columns.11 = 'Drop'
columns.12._label = 'abundance'
columns.12 = 'Expand'
aggfunc = 'sum'
default_0 = False
short_names = True

[save_counts_and_scores]
_uuid = 6ab45c019f6c9c58ddb4d1f4cdeffac4
_module = countess.plugins.csv
_class = SaveCsvPlugin
_version = 0.1.16
_hash = 6bbdd5f2a4797b35bbb0ae501d56194a8e815858938a4bfcdc20ff1d316d14b9
_sort = 0 0
_position = 750 750
_parent.0 = Scale Scores
header = True
filename = '20260217_Lib2_counts_and_scores.csv'
delimiter = ','

[Score Average and Variance]
_uuid = 0d886a1822a3261ecf10d049896a429d
_module = countess.plugins.expression
_class = ExpressionPlugin
_version = 0.1.16
_hash = e361c14eca9724e1d71629047f7ea4e5d4547b417bb815e7226173867a75aad1
_sort = 2 0
_position = 848 500
_parent.0 = pivot_replicates
code = 'abundance_avg = avg(abundance_1, abundance_2, abundance_3)\nvariance = var(abundance_1, abundance_2, abundance_3)\nstd_dev = std(abundance_1, abundance_2, abundance_3)\n\n'

[save_scores]
_uuid = a2d9bdc3405c01ab8847b55cbe5abf22
_module = countess.plugins.csv
_class = SaveCsvPlugin
_version = 0.1.16
_hash = 14ddbf2b7a705aab358b65df5f29835c1bd9d24d7c4f3acf4c6024b56be419b3
_sort = 0 0
_position = 949 500
_parent.0 = Score Average and Variance
header = True
filename = '20260217_TSC2_lib2_scores.csv'
delimiter = ','