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Merge pull request #125 from ncsa/develop
small refactoring for Markov model in development
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Original file line number | Diff line number | Diff line change |
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from .models import * | ||
from .error_models import * | ||
from .mutation_model import * | ||
from .fragment_model import * |
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import numpy as np | ||
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# The following default model parameters are here, for tweaking and revision. | ||
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# This is based on the input model NEAT was using previously | ||
default_error_transition_matrix = np.array( | ||
[[0.0, 0.4918, 0.3377, 0.1705], | ||
[0.5238, 0.0, 0.2661, 0.2101], | ||
[0.3755, 0.2355, 0.0, 0.389], | ||
[0.2505, 0.2552, 0.4943, 0.0]] | ||
) | ||
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# All numbers from 1-42 | ||
default_quality_scores = np.arange(1, 43) | ||
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default_qual_score_probs = np.array([ | ||
[35.20551064, 5.39726466], | ||
[35.05310236, 5.63622973], | ||
[35.03595806, 5.66646784], | ||
[34.98022112, 5.74627755], | ||
[34.97572106, 5.75463045], | ||
[34.4884581, 6.41083843], | ||
[35.01230914, 5.69464369], | ||
[35.05956044, 5.61320501], | ||
[35.06796147, 5.57262371], | ||
[34.96093227, 5.72592418], | ||
[34.94813878, 5.75079686], | ||
[34.96537761, 5.74288137], | ||
[35.04818471, 5.64898391], | ||
[35.05231225, 5.64270542], | ||
[35.01482501, 5.69340856], | ||
[34.9825929, 5.73638614], | ||
[34.98442388, 5.7366054], | ||
[35.03409773, 5.66869673], | ||
[35.0844361, 5.54805317], | ||
[35.08961879, 5.53743692], | ||
[35.0466029, 5.60379104], | ||
[34.99117371, 5.69895578], | ||
[34.9815548, 5.71482919], | ||
[34.98911734, 5.7011922], | ||
[34.93751495, 5.78304943], | ||
[34.93036155, 5.79838573], | ||
[34.92922972, 5.8309752], | ||
[34.96684586, 5.76060028], | ||
[34.9708005, 5.74962913], | ||
[34.95329795, 5.7652556], | ||
[34.92443461, 5.83257523], | ||
[34.91492225, 5.84652014], | ||
[34.8549109, 5.91585614], | ||
[34.94560666, 5.76479635], | ||
[34.96711896, 5.72745932], | ||
[34.88901206, 5.85709602], | ||
[34.93905948, 5.76436017], | ||
[34.94363806, 5.7506911], | ||
[34.89343347, 5.80958086], | ||
[34.95898364, 5.77013784], | ||
[34.9618132, 5.77057502], | ||
[34.9055352, 5.82500424], | ||
[34.95546906, 5.78985858], | ||
[34.96132197, 5.77845029], | ||
[34.87531478, 5.88705352], | ||
[34.84007611, 5.98736108], | ||
[34.84061082, 5.98726021], | ||
[34.89358007, 5.83662558], | ||
[34.88615263, 5.87565349], | ||
[34.88569617, 5.87220656], | ||
[34.80492984, 6.03141243], | ||
[34.88045333, 5.87773523], | ||
[34.86089018, 5.92644241], | ||
[34.85899099, 5.93253766], | ||
[34.85281461, 5.95985895], | ||
[34.8233026, 5.92281158], | ||
[34.81999927, 5.93027502], | ||
[34.86737867, 5.89225314], | ||
[34.84964333, 5.94130026], | ||
[34.8416016, 5.95394121], | ||
[34.83298563, 5.93068537], | ||
[34.85175139, 5.91356723], | ||
[34.85312089, 5.91332882], | ||
[34.81363703, 5.99487116], | ||
[34.84683162, 5.91835211], | ||
[34.8503877, 5.90848694], | ||
[34.75132727, 6.05903999], | ||
[34.69121836, 6.10534185], | ||
[34.69027134, 6.10258631], | ||
[34.55838196, 6.33738628], | ||
[34.66787243, 6.16328276], | ||
[34.67600762, 6.14921298], | ||
[34.69141004, 6.12850504], | ||
[34.69170575, 6.11885946], | ||
[34.69627971, 6.11449364], | ||
[34.61730669, 6.25960228], | ||
[34.65572245, 6.15978888], | ||
[34.66272688, 6.15123117], | ||
[34.61673377, 6.26945453], | ||
[34.50737271, 6.36690753], | ||
[34.49273489, 6.38753577], | ||
[34.53277647, 6.35271811], | ||
[34.55186016, 6.29667187], | ||
[34.5545907, 6.29615587], | ||
[34.42162184, 6.48769325], | ||
[34.42162184, 6.48769325], | ||
[34.41120476, 6.51973428], | ||
[34.41001927, 6.52218756], | ||
[34.50872609, 6.36667517], | ||
[34.34054261, 6.55724021], | ||
[34.31472999, 6.59706435], | ||
[34.44800289, 6.370829], | ||
[34.38082743, 6.48116784], | ||
[34.36736783, 6.50225428], | ||
[34.39091046, 6.49333254], | ||
[34.14685981, 6.81443525], | ||
[34.11286757, 6.86040777], | ||
[34.03892364, 6.9167951], | ||
[34.09461999, 6.84357267], | ||
[34.11624969, 6.81739307], | ||
[34.03311938, 6.89976027], | ||
[34.19285701, 6.73526643], | ||
[34.0871172, 6.85069533], | ||
[34.06668596, 6.8773227], | ||
[33.96060364, 6.9642502], | ||
[33.96399568, 6.94576564], | ||
[33.96784324, 6.94562026], | ||
[33.90260425, 7.05523946], | ||
[33.84443023, 7.10595304], | ||
[33.82584028, 7.12368594], | ||
[33.83180939, 7.14712464], | ||
[33.80809054, 7.14842046], | ||
[33.80740632, 7.14768389], | ||
[33.77340509, 7.16367224], | ||
[33.68690403, 7.30024217], | ||
[33.67144094, 7.32120751], | ||
[33.71053312, 7.25308594], | ||
[33.67084687, 7.25185612], | ||
[33.67146605, 7.24695417], | ||
[33.50354352, 7.43740665], | ||
[33.43878783, 7.43451809], | ||
[33.41994711, 7.45122696], | ||
[33.41239779, 7.46949964], | ||
[33.2412823, 7.64587631], | ||
[33.21334153, 7.67937435], | ||
[33.26008323, 7.62315701], | ||
[33.07948592, 7.80559543], | ||
[33.04336633, 7.83646848], | ||
[33.06584588, 7.77135486], | ||
[32.75754503, 8.02442237], | ||
[32.69941899, 8.08132663], | ||
[32.32145073, 8.41139017], | ||
[32.29822443, 8.37790239], | ||
[32.27939786, 8.38937451], | ||
[32.12769178, 8.50162153], | ||
[31.96975037, 8.62588371], | ||
[31.91995927, 8.66055964], | ||
[31.90028244, 8.63664978], | ||
[31.95031161, 8.63975579], | ||
[31.9793546, 8.62708864], | ||
[32.01732911, 8.59965107], | ||
[31.90794492, 8.63745435], | ||
[31.86247331, 8.66495217], | ||
[31.8237584, 8.71014014], | ||
[31.7715014, 8.75323658], | ||
[31.75047688, 8.77579462], | ||
[31.50448208, 8.92324659], | ||
[31.49927017, 8.91928077], | ||
[31.48842743, 8.92882862], | ||
[30.88872613, 9.25271538], | ||
[28.51071465, 10.2517433] | ||
]) | ||
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