From 3a2ae7519c473242166690b71b39808a3ac59b01 Mon Sep 17 00:00:00 2001 From: Simon Crase Date: Thu, 9 May 2024 12:18:55 +1200 Subject: [PATCH] #92 Tidied up --- BA11F.py | 2 - data/rosalind_ba11f.txt | 4 +- phylogeny.py | 32 +- rosalind.wpr | 655 ++++++++++++++++++++++------------------ spectrum.py | 18 +- 5 files changed, 392 insertions(+), 319 deletions(-) diff --git a/BA11F.py b/BA11F.py index 88ed0a1..14502cf 100644 --- a/BA11F.py +++ b/BA11F.py @@ -20,7 +20,6 @@ from argparse import ArgumentParser from os.path import basename,splitext,join from time import time -import numpy as np from helpers import read_strings from reference_tables import test_masses from spectrum import IdentifyPeptide @@ -49,7 +48,6 @@ Spectral = [int(s) for s in Input[0].split()] Result = IdentifyPeptide(Spectral,Input[1]) - print (Result) with open(f'{basename(__file__).split(".")[0]}.txt','w') as f: f.write(Result) diff --git a/data/rosalind_ba11f.txt b/data/rosalind_ba11f.txt index 49eecf8..9fbdce3 100644 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diff --git a/phylogeny.py b/phylogeny.py index cb88c59..fa9e5be 100644 --- a/phylogeny.py +++ b/phylogeny.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -# Copyright (C) 2020-2023 Greenweaves Software Limited +# Copyright (C) 2020-2024 Greenweaves Software Limited # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -23,19 +23,19 @@ therefore use the name "char" to the Python lexical elements, e.g. "list of chars". ''' -from unittest import TestCase, main, skip -from io import StringIO -from random import randrange -from re import compile -import numpy as np -from Bio.Phylo import read -from scipy.special import comb -from scipy.stats import entropy -from newick import newick_to_adjacency_list, Parser, Tokenizer, Hierarchy -from rosalind import LabeledTree, hamm, Tree, RosalindException -from fasta import FastaContent -from helpers import flatten, expand - +from math import factorial +from unittest import TestCase, main, skip +from io import StringIO +from random import randrange +from re import compile +import numpy as np +from Bio.Phylo import read +from scipy.special import comb +from scipy.stats import entropy +from newick import newick_to_adjacency_list, Parser, Tokenizer, Hierarchy +from rosalind import LabeledTree, hamm, Tree, RosalindException +from fasta import FastaContent +from helpers import flatten, expand def CompleteTree(n, adj): ''' @@ -153,7 +153,7 @@ def NumberBinaryTrees(n, rooted=True): See the equations given in the last slide of http://carrot.mcb.uconn.edu/~olgazh/bioinf2010/class16.html ''' - return np.math.factorial(2*n - 3)/(2**(n-2) * np.math.factorial(n-2)) if rooted else NumberBinaryTrees(n-1) + return factorial(2*n - 3)/(2**(n-2) * factorial(n-2)) if rooted else NumberBinaryTrees(n-1) class UnrootedBinaryTree: @@ -1582,7 +1582,7 @@ def test_ba7a(self): '''BA7A Compute Distances Between Leaves''' def create_weighted_adjacency(n,Edges): T = [[] for _ in range(n+2)] - re_edge = compile('(\d+)->(\d+):(\d+)') + re_edge = compile(r'(\d+)->(\d+):(\d+)') for edge in Edges: matched = re_edge.match(edge) i,node,weight = (int(j) for j in matched.groups()) diff --git a/rosalind.wpr b/rosalind.wpr index 0851e37..271957c 100644 --- a/rosalind.wpr +++ b/rosalind.wpr @@ -465,6 +465,10 @@ proj.launch-config = {loc('2sat.py'): ('project', ('--sample', ''))} [user attributes] +debug.breakpoints = {loc('sequence.py'): {404: (0, + None, + 1, + 0)}} debug.err-values = {loc('BA5H.py'): {}, loc('cte.py'): {}} debug.recent-run-args = {loc('2sat.py'): ['--rosalind', @@ -500,7 +504,8 @@ debug.recent-run-args = {loc('2sat.py'): ['--rosalind', '--rosalind', '--sample'], loc('BA11F.py'): ['--sample', - '--extra'], + '--extra', + '--rosalind'], loc('BA5K.py'): ['--sample', '--align', '--extra'], @@ -757,7 +762,7 @@ debug.show-args-dialog = {loc('../cluster/fcs_params.py'): False, loc('count-kmer-occurrences.py'): False, loc('newick.py'): False, loc('nwck.py'): False, - loc('unknown: #1'): False} + loc('unknown: #59'): False} guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'windows': [{'name': 'dtaAtJloNhSft7SabFzspl0xqEmVIDbK', 'size-state': 'maximized', @@ -775,8 +780,8 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', {'tree-state': {'file-sort-method': 'by name', 'list-files-first': False, 'tree-states': {'deep': {'expanded-nodes': [], - 'selected-nodes': [], - 'top-node': (44,)}}, + 'selected-nodes': [(172,)], + 'top-node': (141,)}}, 'tree-style': 'deep'}}), ('source-assistant', 'tall', @@ -1027,6 +1032,11 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'top-node': [('generic attribute', loc('BA11F.py'), 'args')]}, + loc('BA4M.py'): {'expanded-nodes': [], + 'selected-nodes': [], + 'top-node': [('generic attribute', + loc('BA4M.py'), + 'e')]}, loc('BA5H.py'): {'expanded-nodes': [], 'selected-nodes': [], 'top-node': [('generic attribute', @@ -1057,6 +1067,11 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'top-node': [('generic attribute', loc('BA6B.py'), 'args')]}, + loc('BA6D.py'): {'expanded-nodes': [], + 'selected-nodes': [], + 'top-node': [('generic attribute', + loc('BA6D.py'), + 'args')]}, loc('BA7A.py'): {'expanded-nodes': [], 'selected-nodes': [], 'top-node': [('generic attribute', @@ -1449,7 +1464,7 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'create_adjacency')]], 'top-node': [('function def', loc('helpers.py'), - 'binary')]}, + 'create_adjacency')]}, loc('hmm.py'): {'expanded-nodes': [[('class def', loc('hmm.py'), 'Test_10_HMM')]], @@ -1575,7 +1590,7 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'NumberBinaryTrees')]], 'top-node': [('function def', loc('phylogeny.py'), - 'CharacterTable')]}, + 'AdaptSmallParsimonyToUnrootedTrees')]}, loc('pmch.py'): {'expanded-nodes': [], 'selected-nodes': [], 'top-node': [('generic attribute', @@ -1713,13 +1728,15 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'top-node': [('generic attribute', loc('spec.py'), 'o')]}, - loc('spectrum.py'): {'expanded-nodes': [], + loc('spectrum.py'): {'expanded-nodes': [[('class def', + loc('spectrum.py'), + 'TestSpectrum')]], 'selected-nodes': [[('function def', loc('spectrum.py'), - 'SequencePeptide')]], + 'IdentifyPeptide')]], 'top-node': [('function def', loc('spectrum.py'), - 'complete_spectrum')]}, + 'DecodeIdealSpectrum')]}, loc('sptd.py'): {'expanded-nodes': [], 'selected-nodes': [], 'top-node': [('generic attribute', @@ -1765,11 +1782,11 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'top-node': [('function def', loc('ukkonen.py'), 'build')]}, - loc('unknown: #2'): {'expanded-nodes': [], - 'selected-nodes': [], - 'top-node': [('function def', - loc('unknown: #3'), - 'to_adjacency_matrix')]}}, + loc('unknown: #60'): {'expanded-nodes': [], + 'selected-nodes': [], + 'top-node': [('function def', + loc('unknown: #61'), + 'to_adjacency_matrix')]}}, 'browse_mode': 'Current Module', 'follow-selection': False, 'sort_mode': 'Alphabetically', @@ -1782,7 +1799,7 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', {})], 'primary_view_state': {'area': 'wide', 'constraint': None, - 'current_pages': [3, + 'current_pages': [1, 0], 'notebook_display': 'normal', 'notebook_percent': 0.2985318107667211, @@ -1802,7 +1819,7 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'fRegexFlags': 40, 'fReplaceText': 'get_highest_scoring_alignment', 'fReverse': False, - 'fSearchText': 'args.extra', + 'fSearchText': 'flatten', 'fStartPos': 0, 'fStyle': 'text', 'fWholeWords': False, @@ -1833,7 +1850,7 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'fRegexFlags': 42, 'fReplaceText': 'get_cyclo_spectrum', 'fReverse': False, - 'fSearchText': 'splite', + 'fSearchText': 'argv', 'fStartPos': 0, 'fStyle': 'text', 'fWholeWords': False, @@ -1886,276 +1903,315 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', {'last-percent': 0.8, 'toolbox-percent': 1.0, 'toolbox-tree-sel': ''})], - 'primary_view_state': {'editor_states': ({'bookmarks': ([[loc('spectrum.py'), - {'attrib-starts': [('CreatePeptideVector|0|', - 135)], - 'code-line': ' masses = [extended_masses[p] for p in peptide]\r\n', - 'first-line': 175, + 'primary_view_state': {'editor_states': ({'bookmarks': ([[loc('sequence.py'), + {'attrib-starts': [('mostProbable|0|', + 90)], + 'code-line': ' def findMostProbable():\r\n', + 'first-line': 91, 'folded-linenos': [], - 'sel-line': 159, - 'sel-line-start': 5751, - 'selection_end': 5801, - 'selection_start': 5755, + 'sel-line': 102, + 'sel-line-start': 3148, + 'selection_end': 3165, + 'selection_start': 3160, 'zoom': 0}, - 1715159059.8124402], - [loc('BA11F.py'), - {'attrib-starts': [], - 'code-line': 'from spectrum import compute_scores, invert\r\n', - 'first-line': 15, + 1715212674.7070217], + [loc('sequence.py'), + {'attrib-starts': [('mostProbable|0|', + 90)], + 'code-line': ' return findMostProbable()\r\n', + 'first-line': 91, 'folded-linenos': [], - 'sel-line': 25, - 'sel-line-start': 1045, - 'selection_end': 1081, - 'selection_start': 1067, + 'sel-line': 106, + 'sel-line-start': 3304, + 'selection_end': 3324, + 'selection_start': 3319, 'zoom': 0}, - 1715159073.5398233], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1040, + 1715212675.6629486], + [loc('sequence.py'), + {'attrib-starts': [('greedyMotifSearch|0|', + 109)], + 'code-line': ' motifs.append(mostProbable(dna[i],k,profile(motifs)))\r\n', + 'first-line': 136, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 153, + 'sel-line-start': 4940, + 'selection_end': 4971, + 'selection_start': 4966, 'zoom': 0}, - 1715159119.1700933], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 30, + 1715212677.2680893], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365), + ('Test_2_Sequence|0|.test_ba2b|0|', + 377)], + 'code-line': " 'AAATTGACGCAT',\r\n", + 'first-line': 376, 'folded-linenos': [], - 'sel-line': 46, - 'sel-line-start': 1776, - 'selection_end': 1795, - 'selection_start': 1795, + 'sel-line': 381, + 'sel-line-start': 11942, + 'selection_end': 11963, + 'selection_start': 11963, 'zoom': 0}, - 1715159140.9644973], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1040, + 1715212817.5700517], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365), + ('Test_2_Sequence|0|.test_ba2b|0|', + 377)], + 'code-line': " 'AAATTGACGCAT',\r\n", + 'first-line': 93, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 381, + 'sel-line-start': 11942, + 'selection_end': 11963, + 'selection_start': 11963, 'zoom': 0}, - 1715159156.949093], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' score = 0\r\n', - 'first-line': 30, + 1715212890.4669354], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365)], + 'code-line': ' def test_ba2a(self):\r\n', + 'first-line': 361, 'folded-linenos': [], - 'sel-line': 48, - 'sel-line-start': 1840, - 'selection_end': 1857, - 'selection_start': 1857, + 'sel-line': 367, + 'sel-line-start': 11323, + 'selection_end': 12096, + 'selection_start': 11325, 'zoom': 0}, - 1715159193.626407], - [loc('BA11E.py'), - {'attrib-starts': [], - 'code-line': ' protein_masses=test_masses))\r\n', - 'first-line': 21, + 1715212898.090617], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365)], + 'code-line': ' def test_ba2e(self):\r\n', + 'first-line': 396, 'folded-linenos': [], - 'sel-line': 36, - 'sel-line-start': 1605, - 'selection_end': 1646, - 'selection_start': 1619, + 'sel-line': 415, + 'sel-line-start': 13337, + 'selection_end': 13524, + 'selection_start': 13341, 'zoom': 0}, - 1715159196.6988275], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1040, + 1715212925.6030793], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365), + ('Test_2_Sequence|0|.test_ba2d|0|', + 401)], + 'code-line': ' # def test_ba2e(self):\r\n', + 'first-line': 448, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 415, + 'sel-line-start': 13337, + 'selection_end': 15701, + 'selection_start': 13337, 'zoom': 0}, - 1715193672.3923068], - [loc('BA11C.py'), - {'attrib-starts': [], - 'code-line': " print(' '.join(str(i) for i in CreatePeptideVector('STEQVPNQPYVWIHACNGVTADIFRAFHQVHFK')))\r\n", - 'first-line': 1, + 1715212950.4771016], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365)], + 'code-line': " # ['ATTTGGC',\r\n", + 'first-line': 358, 'folded-linenos': [], - 'sel-line': 22, - 'sel-line-start': 881, - 'selection_end': 935, - 'selection_start': 916, + 'sel-line': 372, + 'sel-line-start': 11562, + 'selection_end': 11620, + 'selection_start': 11620, 'zoom': 0}, - 1715193680.4554417], - [loc('BA11E.py'), - {'attrib-starts': [], - 'code-line': ' protein_masses=test_masses))\r\n', - 'first-line': 21, + 1715213004.0421915], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365), + ('Test_2_Sequence|0|.test_ba2d|0|', + 401)], + 'code-line': ' motifs=greedyMotifSearch(3,\r\n', + 'first-line': 394, 'folded-linenos': [], - 'sel-line': 36, - 'sel-line-start': 1605, - 'selection_end': 1646, - 'selection_start': 1619, + 'sel-line': 403, + 'sel-line-start': 12863, + 'selection_end': 12899, + 'selection_start': 12882, 'zoom': 0}, - 1715193693.0556445], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' for j in range(i+1,len(proteome_masses)):\r\n', - 'first-line': 40, + 1715213052.9714088], + [loc('sequence.py'), + {'attrib-starts': [('greedyMotifSearch|0|', + 109)], + 'code-line': ' GreedyMotifSearch(Dna, k, t). If at any step you find more than one\r\n', + 'first-line': 101, 'folded-linenos': [], - 'sel-line': 49, - 'sel-line-start': 1859, - 'selection_end': 1882, - 'selection_start': 1882, + 'sel-line': 118, + 'sel-line-start': 3736, + 'selection_end': 3752, + 'selection_start': 3752, 'zoom': 0}, - 1715193696.3465736], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1040, + 1715213097.8964746], + [loc('sequence.py'), + {'attrib-starts': [('Test_2_Sequence|0|', + 365), + ('Test_2_Sequence|0|.test_ba2d|0|', + 401)], + 'code-line': ' motifs=greedyMotifSearch(3,\r\n', + 'first-line': 396, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 403, + 'sel-line-start': 12803, + 'selection_end': 12839, + 'selection_start': 12822, 'zoom': 0}, - 1715193719.7164185], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' candidate.append()\r\n', - 'first-line': 38, + 1715213164.262793], + [loc('sequence.py'), + {'attrib-starts': [], + 'code-line': 'def greedyMotifSearch(k,t,dna,pseudo_counts=False):\r\n', + 'first-line': 95, 'folded-linenos': [], - 'sel-line': 56, - 'sel-line-start': 2149, - 'selection_end': 2178, - 'selection_start': 2178, + 'sel-line': 109, + 'sel-line-start': 3340, + 'selection_end': 3361, + 'selection_start': 3344, 'zoom': 0}, - 1715194786.558268], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' return None\r\n', - 'first-line': 42, + 1715213207.2767396], + [loc('sequence.py'), + {'attrib-starts': [], + 'code-line': 'def greedyMotifSearch(k,t,dna,pseudo_counts=False):\r\n', + 'first-line': 0, 'folded-linenos': [], - 'sel-line': 59, - 'sel-line-start': 2302, - 'selection_end': 2302, - 'selection_start': 2302, + 'sel-line': 109, + 'sel-line-start': 3340, + 'selection_end': 3361, + 'selection_start': 3344, 'zoom': 0}, - 1715195892.248308], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' if index >= n: break\r\n', - 'first-line': 57, + 1715213378.0087245], + [loc('phylogeny.py'), + {'attrib-starts': [('rsub|0|', + 1188), + ('rsub|0|.create_parents|0|', + 1246)], + 'code-line': ' Product = {node:[] for node in flatten(Adj.values())}\r\n', + 'first-line': 1236, 'folded-linenos': [], - 'sel-line': 52, - 'sel-line-start': 2051, - 'selection_end': 2083, - 'selection_start': 2083, + 'sel-line': 1252, + 'sel-line-start': 44033, + 'selection_end': 44079, + 'selection_start': 44072, 'zoom': 0}, - 1715201216.4225993], - [loc('BA11F.py'), + 1715213389.3724515], + [loc('helpers.py'), {'attrib-starts': [], - 'code-line': ' print (IdentifyPeptide(Spectral,Input[1]))\r\n', - 'first-line': 66, + 'code-line': 'def flatten(x):\r\n', + 'first-line': 91, 'folded-linenos': [], - 'sel-line': 77, - 'sel-line-start': 3275, - 'selection_end': 3323, - 'selection_start': 3323, + 'sel-line': 102, + 'sel-line-start': 2887, + 'selection_end': 2898, + 'selection_start': 2891, 'zoom': 0}, - 1715202864.8805578], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1040, + 1715213399.4034805], + [loc('helpers.py'), + {'attrib-starts': [], + 'code-line': '\r\n', + 'first-line': 3, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 15, + 'sel-line-start': 704, + 'selection_end': 704, + 'selection_start': 704, 'zoom': 0}, - 1715202873.394631], - [loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1076, + 1715213456.9530218], + [loc('helpers.py'), + {'attrib-starts': [], + 'code-line': 'from sys import argv\r\n', + 'first-line': 11, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 22, + 'sel-line-start': 884, + 'selection_end': 906, + 'selection_start': 904, 'zoom': 0}, - 1715202880.884859], - [loc('BA11F.py'), + 1715213457.9174573], + [loc('helpers.py'), {'attrib-starts': [], - 'code-line': ' print (IdentifyPeptide([0, 0, 0, 4, -2, -3, -1, -7, 6, 5, 3, 2, 1, 9, 3, -8, 0, 3, 1, 2, 1, 8],\r\n', - 'first-line': 66, + 'code-line': 'from sys import argv\r\n', + 'first-line': 11, 'folded-linenos': [], - 'sel-line': 70, - 'sel-line-start': 2904, - 'selection_end': 2934, - 'selection_start': 2919, + 'sel-line': 22, + 'sel-line-start': 884, + 'selection_end': 908, + 'selection_start': 904, 'zoom': 0}, - 1715202892.47871], - [loc('BA11F.py'), - {'attrib-starts': [('IdentifyPeptide|0|', - 27)], - 'code-line': ' # print (i,k, i+k, index, proteome_masses[i + k], S0, candidate,score)\r\n', - 'first-line': 49, + 1715213460.8807025], + [loc('helpers.py'), + {'attrib-starts': [('parse_graphs|0|', + 111)], + 'code-line': ' return product\r\n', + 'first-line': 128, 'folded-linenos': [], - 'sel-line': 61, - 'sel-line-start': 2326, - 'selection_end': 2329, - 'selection_start': 2329, + 'sel-line': 141, + 'sel-line-start': 4052, + 'selection_end': 4070, + 'selection_start': 4070, 'zoom': 0}, - 1715204671.4315557]], + 1715213478.6003606]], 20), - 'current-loc': loc('BA11F.py'), + 'current-loc': loc('helpers.py'), 'editor-state-list': [(loc('BA11F.py'), {'attrib-starts': [], - 'code-line': ' f.write(Result)\r\n', - 'first-line': 76, + 'code-line': 'from helpers import read_strings\r\n', + 'first-line': 12, + 'folded-linenos': [], + 'sel-line': 22, + 'sel-line-start': 933, + 'selection_end': 965, + 'selection_start': 953, + 'zoom': 0}), + (loc('helpers.py'), + {'attrib-starts': [('parse_graphs|0|', + 111)], + 'code-line': ' return product\r\n', + 'first-line': 12, 'folded-linenos': [], - 'sel-line': 93, - 'sel-line-start': 3856, - 'selection_end': 3883, - 'selection_start': 3883, + 'sel-line': 141, + 'sel-line-start': 4052, + 'selection_end': 4070, + 'selection_start': 4070, + 'zoom': 0}), + (loc('phylogeny.py'), + {'attrib-starts': [('rsub|0|', + 1188), + ('rsub|0|.create_parents|0|', + 1246)], + 'code-line': ' Product = {node:[] for node in flatten(Adj.values())}\r\n', + 'first-line': 1236, + 'folded-linenos': [], + 'sel-line': 1252, + 'sel-line-start': 44033, + 'selection_end': 44079, + 'selection_start': 44072, 'zoom': 0}), (loc('spectrum.py'), - {'attrib-starts': [('compute_scores|0|', - 1036)], - 'code-line': ' n = len(Scores)\r\n', - 'first-line': 1076, + {'attrib-starts': [], + 'code-line': 'def IdentifyPeptide(S,Proteome,protein_masses = integer_masses):\r\n', + 'first-line': 1120, 'folded-linenos': [], - 'sel-line': 1050, - 'sel-line-start': 40559, - 'selection_end': 40578, - 'selection_start': 40559, + 'sel-line': 1095, + 'sel-line-start': 42562, + 'selection_end': 42581, + 'selection_start': 42566, 'zoom': 0})], 'has-focus': True, 'locked': False}, [loc('BA11F.py'), + loc('helpers.py'), + loc('phylogeny.py'), loc('spectrum.py')]), 'open_files': ['spectrum.py', - 'BA11F.py']}, + 'BA11F.py', + 'phylogeny.py', + 'helpers.py']}, 'saved_notebook_display': None, 'split_percents': {0: 0.5}, 'splits': 2, 'tab_location': 'top', - 'traversal_pos': ((1, - 0), - 1715204528.324618), + 'traversal_pos': ((0, + 1), + 1715213454.9021592), 'user_data': {}}, 'saved_notebook_display': None, 'split_percents': {}, @@ -2163,13 +2219,15 @@ guimgr.overall-gui-state = {'windowing-policy': 'combined-window', 'tab_location': 'left', 'traversal_pos': ((0, 0), - 1715141291.4798405), + 1715208999.9188104), 'user_data': {}}, 'window-alloc': (25, 399, 1298, 335)}]} -guimgr.recent-documents = [loc('BA11F.py'), +guimgr.recent-documents = [loc('helpers.py'), + loc('phylogeny.py'), + loc('BA11F.py'), loc('spectrum.py')] guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): {'attrib-starts': [('as_handle', 57)], @@ -2482,15 +2540,15 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'zoom': 0}, loc('../AppData/Local/Programs/Python/Python312/Lib/unittest/case.py'): {'attrib-starts': [('TestCase|0|', 344), - ('TestCase|0|._baseAssertEqual|0|', - 872)], - 'code-line': ' raise self.failureException(msg)\r\n', - 'first-line': 872, + ('TestCase|0|.fail|0|', + 712)], + 'code-line': ' raise self.failureException(msg)\r\n', + 'first-line': 709, 'folded-linenos': [], - 'sel-line': 877, - 'sel-line-start': 34039, - 'selection_end': 34039, - 'selection_start': 34039, + 'sel-line': 714, + 'sel-line-start': 26527, + 'selection_end': 26527, + 'selection_start': 26527, 'zoom': 0}, loc('../AppData/Local/Programs/Python/Python38/Lib/site-packages/Bio/File.py'): {'attrib-starts': [('as_handle|0|', 28)], @@ -2749,13 +2807,13 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_start': 984, 'zoom': 0}, loc('BA10J.py'): {'attrib-starts': [], - 'code-line': ' for line in SoftDecode(xs,alphabet,States,Transition,Emission).probabilities:\r\n', - 'first-line': 39, + 'code-line': 'from helpers import create_hmm_from_strings, read_strings, format_list\r\n', + 'first-line': 10, 'folded-linenos': [], - 'sel-line': 53, - 'sel-line-start': 2509, - 'selection_end': 2597, - 'selection_start': 2597, + 'sel-line': 22, + 'sel-line-start': 889, + 'selection_end': 960, + 'selection_start': 949, 'zoom': 0}, loc('BA10K.py'): {'attrib-starts': [], 'code-line': ' Transitions,Emissions = BaumWelch(xs,alphabet,States,Transition,Emission,N=100)\r\n', @@ -3072,14 +3130,15 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_end': 23, 'selection_start': 23, 'zoom': 0}, - loc('BA8E.py'): {'attrib-starts': [], - 'code-line': '# Copyright (C) 2017 Greenweaves Software Pty Ltd\r\n', - 'first-line': 9, + loc('BA8E.py'): {'attrib-starts': [('format|0|', + 21)], + 'code-line': ' def expand(links):\r\n', + 'first-line': 10, 'folded-linenos': [], - 'sel-line': 2, - 'sel-line-start': 25, - 'selection_end': 26, - 'selection_start': 25, + 'sel-line': 22, + 'sel-line-start': 829, + 'selection_end': 841, + 'selection_start': 835, 'zoom': 0}, loc('BA9A.py'): {'attrib-starts': [], 'code-line': '# Copyright (C) 2019-2020 Greenweaves Software Limited\r\n', @@ -3515,13 +3574,13 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_start': 23, 'zoom': 0}, loc('bip.py'): {'attrib-starts': [], - 'code-line': 'from graphs import bip\r\n', - 'first-line': 12, + 'code-line': ' print (format_list([bip(g) for g in parse_graphs(f)]))\r\n', + 'first-line': 8, 'folded-linenos': [], - 'sel-line': 19, - 'sel-line-start': 824, - 'selection_end': 846, - 'selection_start': 843, + 'sel-line': 25, + 'sel-line-start': 950, + 'selection_end': 1005, + 'selection_start': 994, 'zoom': 0}, loc('bryant.py'): {'attrib-starts': [], 'code-line': '', @@ -3857,15 +3916,17 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_end': 1224, 'selection_start': 1224, 'zoom': 0}, - loc('hmm.py'): {'attrib-starts': [('BaumWelch|0|', - 554)], - 'code-line': ' Emission Probabilities of symbols being emitted in each state updated\r\n', - 'first-line': 601, + loc('hmm.py'): {'attrib-starts': [('Test_10_HMM|0|', + 631), + ('Test_10_HMM|0|.test_ba10e2|0|', + 713)], + 'code-line': ' Transition, Emission,StateNames = ConstructProfileHMM(0.289,\r\n', + 'first-line': 702, 'folded-linenos': [], - 'sel-line': 567, - 'sel-line-start': 19390, - 'selection_end': 19401, - 'selection_start': 19401, + 'sel-line': 714, + 'sel-line-start': 26500, + 'selection_end': 26542, + 'selection_start': 26538, 'zoom': 0}, loc('in.txt'): {'attrib-starts': [], 'first-line': 0, @@ -4296,13 +4357,13 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_start': 23, 'zoom': 0}, loc('sequence.py'): {'attrib-starts': [], - 'code-line': '# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r\n', - 'first-line': 449, + 'code-line': 'def greedyMotifSearch(k,t,dna,pseudo_counts=False):\r\n', + 'first-line': 0, 'folded-linenos': [], - 'sel-line': 11, - 'sel-line-start': 460, - 'selection_end': 470, - 'selection_start': 470, + 'sel-line': 109, + 'sel-line-start': 3340, + 'selection_end': 3361, + 'selection_start': 3344, 'zoom': 0}, loc('sgra.py'): {'attrib-starts': [], 'code-line': '# Copyright (C) 2019 Greenweaves Software Limited\r\n', @@ -4431,13 +4492,13 @@ guimgr.visual-state = {loc('../../../Anaconda3/lib/site-packages/Bio/File.py'): 'selection_start': 23, 'zoom': 0}, loc('ts.py'): {'attrib-starts': [], - 'code-line': 'from align import topological_order\r\n', - 'first-line': 18, + 'code-line': 'from helpers import parse_graph, create_adjacency, format_list\r\n', + 'first-line': 7, 'folded-linenos': [], - 'sel-line': 18, - 'sel-line-start': 777, - 'selection_end': 812, - 'selection_start': 795, + 'sel-line': 19, + 'sel-line-start': 814, + 'selection_end': 863, + 'selection_start': 847, 'zoom': 0}, loc('tyrocidine.py'): {'attrib-starts': [], 'code-line': 'from reference_tables import amino_acids\r\n', @@ -4481,23 +4542,23 @@ search.replace-history = ['get_cyclo_spectrum', 'remaining_edges', 'species_index', '#125'] -search.search-history = ['splite', - 'joi', - 'args.extra', - 'args.', - 'args', - 'fibo', - 'SequencePeptide', - 'score', - 'countMatchesInSpectra', - 'cycloSpectrum', - 'get_cyclo_spectrum', - 'get_cycle_spectrum', - 'cycloSpectrum1', - 'ba4a', - 'ba4', - 'ba', - 'dna_to', - 'sqrt', - 'ceil', - 'log10'] +search.search-history = ['argv', + 'mostP', + 'flatten', + 'flatte', + 'flatt', + 'f', + 'parse_graph', + 'parse_grap', + 'parse_gra', + 'parse_gr', + 'parse_g', + 'parse_', + 'parse', + 'Length', + 'Name', + 'create_adjacency', + 'format_list', + 'print_adjacency_graph', + 'read_list', + 'print_peptide'] diff --git a/spectrum.py b/spectrum.py index d727281..b6775eb 100644 --- a/spectrum.py +++ b/spectrum.py @@ -2900,7 +2900,7 @@ def test_ba11f(self): protein_masses=test_masses)) def test_ba11f_extra(self): - '''BA11E Sequence a Peptide''' + '''BA11E Sequence a Peptide -- extra test''' self.assertEqual('QLEAARSCFSTRNE', IdentifyPeptide([ -10, 8, -15, -8, 28, 29, 8, -17, -8, 19, 6, -9, 7, 16, -15, -13, -9, 29, 21, 17, -12, 28, 22, @@ -2941,7 +2941,21 @@ def test_ba11f_extra(self): 'WCFFGKQIDFIICTNPFTKRDCRLDHNTHSNKMYRNVSNAHTTCFKYKYFYHKNKMCFWLNVEPAKCVAWAEFICWTIVMCFFRVQKEQFPQEC' 'WMMIIVTSNLDAFPDNSRQKRIGETDPQQHMGKWHRHARDKGCMPREQTWQDKFCTYDPSAEDKYQDCYLISAFTWQYWMEQCCYKPRHDPWLN' 'KLQPQFLMSIDSPNPCFSCINHPDECKVGYKHVSRGRPMEQHCKMQPIQNAFLPRFALQHNSQHSWWWIANWQDKMSARWPRLLRTHCVIVNAW' - 'QACNYNDRHCYHFLTFVMYSGFDQNCELRACVVIQCNRTGDYHNQKVYLMIMANHIMLVPRARWFTPQRCINMIECKKNSEANDQYQRLIEFTPWGVEGHEIPNERILQTRHLLLYCMVYQQVQYAKGHEAAIWWFWDTGRIAYCLCLVLRCYWEPESQTTLLTLGAGNNDKMIHNMTFVETYAMPSVASILEKVQMNPDMIMVNEWHKAVWVWDISTLACFHEHHIHPMSICKLIWMSENRFKNFHCPTYGYITRCAYMAQRDYENKHAIWVGTTKFFKTFGFLGYHCPQRIVIEHLIYRPCSTLWCPNWDKKRCQRRGRQQPYANQLSCIAGNGESRIFWTWPQRQIYLYGFHDNHNQMIYLPTSILHSKSNGYAPQFRQYRLSMETMMMTGHQTKPHDWHNKHIHCCYEHDIFLKFVKEVEMYCFNGNNARREIDFQIKYYKHSAFLFQVNMHLYWFKQCGNMSAGNSFRSYKHESFLLYNRDYMKLLLCCDQCDVWCPYNCDRIITCKAGIIIQMATEYPDSQFAVFERGVDDYRVLGDFDAYDAYNTNHVVWQDAYNMWFYNLGPYAMGRQACKPCRGFHGYVMWWEWMALAGGGSIHSYRSERGCASFFWQPNTCGFYGLAMENYREFLCQMDMVVRNKVSDYNTYMMYDWCKPFANLSMFNCKQPMQKTYHLTFGKLEVDVANYMVLFKLHFGCISCDDERLWDMMGRRQVDNMCKEPRPFGFIYYQQTEFWEGLADVTAQYKLNIGKFTMHQELPVPKDNLMNWECSRWFEECHFTQNLFKLRVHYGFAGSALTKVDNCHYSEIQPFTFGKCQCWSDVLKTLQTMYGLNHMYEDEWEYHILETTFCYGNQNMNPFMAHAWFPYSSWQPNHYRPKWLRHLTNMRSGQDMVTRVVCNCANVLDGIHSRIPFFIPSMKSRYFVTSTMPECPFPQMNSWAQIASTYQYKTPWSGLVQGFENDPFAHLYVWFARNWDMYRQSGRCAMYFVKSMSHIIIMCAVHGDLHPQCVAYNHYKTPNAEDCNRDNPDSHYFNTANMDEWPTSHTTFNMYHLIDMCSDPVANCHMVCVQSPCLNEDTGLRTKTEYGTMAEHTSDQKTYQCCGMENYSTVRYNSVEHFWMTWNRNHKVWEMCNIFYSHTFWYVPWLIHTQYPGRAGSTVKQKWTNIGLAACIVYESYFVEGKVELIRQRFHNPTIRTKNPAFTPCIGFTLYTYMEEEVKMHLGVRNNYEYNMSEPDCAQKLREFQEVEIHRMAKGLIVTNAHHCFSMAFYQHSYGKIHVSKSKGHQCCQPGYGPSYEGPTVPKSRKLNQKGAYGHPPDQNEYHNRPENGYCECNVCWEQNTVDTPSPTDGLHVHHVCVPGWVNSGGTEDEWHWQTYMVMTDHFKLYQAQEYPSIWQRQSCQWFCECDGHAPEKMADMYAWGPDHNFGSEMIRPRRCLPCRKGNTAQEVVGMMQENESWANWGIWPMQSQYRIINMTSEMIDSTKYQQGFMFKGQHCSFQKWSQTESEFKSIYGHETRLAVGFLWWENWIWLREYIRPAGMAGCEDEYFTVYPWEPVASRYHWDWEPKTMDCQSKYPIRWDKDDQKWMFNYLIWPQVNDGPMAQSQSHRREQYKYHLYDTNGCQWEFQTPHKPHEYSIQQWKDWYFYNRMKGISCNFDNVSTLPFMNHQPVFCEHFEGRQAHWCQCIFNCYELGEFDYMQWVMVKYAKIKHNPTHTQEVNVWNCWCTPQCICQWMDFPCWWRCFMTCWETMYPGRMSHRMPTLQFLYIEDHVVLMNYSEGKDHWGCKVHPGDRPHVIIDDNPHDMWVWVKGDMIAYIKMVQNQRVCMALYQLWALKQWYYMKWMNDETLSFWEWCGAPGWFIGGADRQRKIFWCWVIGDHPNPGFSSGAVCYDLIRLYDMITPFDYTAESRQLNKYNSRIEGITFVGQRIQLQMIKMGVPIQQPGTWPMAFDMFWDPIHMQWSWNQKFGFGEIYICHFVGGFAAYMIQNWQIQYVEVLASPRYHQDGIKVHHFLESDQSCTMNNPKIHLDFALGEHFPWTRIHAPSCHFYRNQCLWLVIQHQISQHCWMKCQWAFCLKQTKNILHKESYSVCSAEIAMWTIRGRYLAVRASELIAIIGHELPIQGTYRITANAKDEQCTLRGLKVYYSKKRGEKDVDNCIYEIANGIWTQLNIFVRADWSPMAEWGSLSFYMFPNVDDLYRCHDYVMSYMYYFPQRIYWATCKDWEAKLPRVAENVCRDHMHMGHKRWFHGTEQRRHVLQDQICQKTDRYERWRNDQDQNQMQSGPCYCSSHYFCNEWGQTERFIKYEPKNQSFPRHNYLKRHMKPEEANARSESRYCEMSGQFLWLGLENSKHLVRSERWSRDKYYQKFIARIAAHDKILMINYWRATKGAMSHKRTGPQDGVCIWVCWNSKVRMQGYDCTNNACCWCPSCAAMIKENILNYTHAVNTRVWQFNYITRDYQDCWKERNIRQQPWHRFHSCLQLCCHDFIIDKTTLVDFGSLVCARLHPQCNVVYYKAQINRRFMTDCIDVTIVVWPKQEKNAFGRHHQALFPRGHYSGADCVIFDHTKILRIDLSKPHESHWWKYHLPKIAFAGHSVDDPIFIIYMCNHRVPSWAMAWWVKHLTSSMGVFRCISWCNQHLTRTIRKLMYSFGGAPSLPFQMFGINSLEVPNCVTPFIDYRSRVMSDNHSPLKVDVNIMKWQTEYFKGLWCEMTHMERIDYKLCRQFETWCCDMQHSKMPGQMPFIFVFDEMLIFQTPRPDTYENYYRIIGEMHRNYACWPIAFPHDDLPHTVVLKFANNCFRWHDQVINYFGLFVKVYACLPLWVLLLHCEWMMHRVSRMNVCGPILPCEKADILQVKSHEMFPGANGECPYWDPGSCHDAVACCFAKGGEHCGSEMMNKPANTKCHPSANSMWQRHASPRQIIAANHCIALGKERGYHPLQKKHAWRGLEPQWHKSTYKQRCCPMICADIMVDMTWDAHQWGSNFRDEPIYCWAINTHGLHHEIFCYAILHDHCGEHTMVHWVMFNIPPMQHWKVRHEHPGCRGVMDEPSLVFFSSDGSNWIKVTSEALFVDIYPQQPKGDAWEVCKQEPPEISELGSEHSANASCNNFIYSGTKTFRMDNQGECSNKAFALCFIMCIWCTYTEKYMAPRNAVLSKADCSPIWMEEILFVFMPAYYPGDIFPWMAEKDCIYAMTDNNHDDPVRCECKSEAQEQIMCMPSHFKCRSYVVKRHMSGAPETIGFAWKPCNNGTLMVLKATLAFGYSCGCYLITRSLAQHYMNIYEYIIAMDWCRGMGNEIHPVIDDSCKTRDVTIHCHKDVMWPGEMEENEGCRWVLCVIKQMQVMIFWDINTYHSVNSARIKWRGKFTCGATGHDGWKCCACDEYRIMEFLDLDWQEGGRQMFACVPANSMPFCIFLVVVGYTICHSIICDTNYGYWECPSSECIRVKKSTLYILASHISYKRTTTDLSHYFMMTYYYEFCEVLTMVQTMNSKVVRDYHAEHVQPRVNAVYGPNSYETIVGHERFLTWTCAKWWSSVWNLEMDRRFMLQLFRCEISMQMLFKVQPYYMARACNYGVGYMWEGTATVACLGKVCNVAVFKFEPFCKMLDRPTIQPDIIYNATIYIDDLDSDKICYMSICVYFYNLVSYYSAHEDFAVCIQHITWELDVFGQNDYMELVIGHI', + 'QACNYNDRHCYHFLTFVMYSGFDQNCELRACVVIQCNRTGDYHNQKVYLMIMANHIMLVPRARWFTPQRCINMIECKKNSEANDQYQRLIEFTP' + 'WGVEGHEIPNERILQTRHLLLYCMVYQQVQYAKGHEAAIWWFWDTGRIAYCLCLVLRCYWEPESQTTLLTLGAGNNDKMIHNMTFVETYAMPSV' + 'ASILEKVQMNPDMIMVNEWHKAVWVWDISTLACFHEHHIHPMSICKLIWMSENRFKNFHCPTYGYITRCAYMAQRDYENKHAIWVGTTKFFKTF' + 'GFLGYHCPQRIVIEHLIYRPCSTLWCPNWDKKRCQRRGRQQPYANQLSCIAGNGESRIFWTWPQRQIYLYGFHDNHNQMIYLPTSILHSKSNGY' + 'APQFRQYRLSMETMMMTGHQTKPHDWHNKHIHCCYEHDIFLKFVKEVEMYCFNGNNARREIDFQIKYYKHSAFLFQVNMHLYWFKQCGNMSAGN' + 'SFRSYKHESFLLYNRDYMKLLLCCDQCDVWCPYNCDRIITCKAGIIIQMATEYPDSQFAVFERGVDDYRVLGDFDAYDAYNTNHVVWQDAYNMW' + 'FYNLGPYAMGRQACKPCRGFHGYVMWWEWMALAGGGSIHSYRSERGCASFFWQPNTCGFYGLAMENYREFLCQMDMVVRNKVSDYNTYMMYDWC' + 'KPFANLSMFNCKQPMQKTYHLTFGKLEVDVANYMVLFKLHFGCISCDDERLWDMMGRRQVDNMCKEPRPFGFIYYQQTEFWEGLADVTAQYKLN' + 'IGKFTMHQELPVPKDNLMNWECSRWFEECHFTQNLFKLRVHYGFAGSALTKVDNCHYSEIQPFTFGKCQCWSDVLKTLQTMYGLNHMYEDEWEY' + 'HILETTFCYGNQNMNPFMAHAWFPYSSWQPNHYRPKWLRHLTNMRSGQDMVTRVVCNCANVLDGIHSRIPFFIPSMKSRYFVTSTMPECPFPQM' + 'NSWAQIASTYQYKTPWSGLVQGFENDPFAHLYVWFARNWDMYRQSGRCAMYFVKSMSHIIIMCAVHGDLHPQCVAYNHYKTPNAEDCNRDNPDS' + 'HYFNTANMDEWPTSHTTFNMYHLIDMCSDPVANCHMVCVQSPCLNEDTGLRTKTEYGTMAEHTSDQKTYQCCGMENYSTVRYNSVEHFWMTWNR' + 'NHKVWEMCNIFYSHTFWYVPWLIHTQYPGRAGSTVKQKWTNIGLAACIVYESYFVEGKVELIRQRFHNPTIRTKNPAFTPCIGFTLYTYMEEEV' + 'KMHLGVRNNYEYNMSEPDCAQKLREFQEVEIHRMAKGLIVTNAHHCFSMAFYQHSYGKIHVSKSKGHQCCQPGYGPSYEGPTVPKSRKLNQKGA' + 'YGHPPDQNEYHNRPENGYCECNVCWEQNTVDTPSPTDGLHVHHVCVPGWVNSGGTEDEWHWQTYMVMTDHFKLYQAQEYPSIWQRQSCQWFCECDGHAPEKMADMYAWGPDHNFGSEMIRPRRCLPCRKGNTAQEVVGMMQENESWANWGIWPMQSQYRIINMTSEMIDSTKYQQGFMFKGQHCSFQKWSQTESEFKSIYGHETRLAVGFLWWENWIWLREYIRPAGMAGCEDEYFTVYPWEPVASRYHWDWEPKTMDCQSKYPIRWDKDDQKWMFNYLIWPQVNDGPMAQSQSHRREQYKYHLYDTNGCQWEFQTPHKPHEYSIQQWKDWYFYNRMKGISCNFDNVSTLPFMNHQPVFCEHFEGRQAHWCQCIFNCYELGEFDYMQWVMVKYAKIKHNPTHTQEVNVWNCWCTPQCICQWMDFPCWWRCFMTCWETMYPGRMSHRMPTLQFLYIEDHVVLMNYSEGKDHWGCKVHPGDRPHVIIDDNPHDMWVWVKGDMIAYIKMVQNQRVCMALYQLWALKQWYYMKWMNDETLSFWEWCGAPGWFIGGADRQRKIFWCWVIGDHPNPGFSSGAVCYDLIRLYDMITPFDYTAESRQLNKYNSRIEGITFVGQRIQLQMIKMGVPIQQPGTWPMAFDMFWDPIHMQWSWNQKFGFGEIYICHFVGGFAAYMIQNWQIQYVEVLASPRYHQDGIKVHHFLESDQSCTMNNPKIHLDFALGEHFPWTRIHAPSCHFYRNQCLWLVIQHQISQHCWMKCQWAFCLKQTKNILHKESYSVCSAEIAMWTIRGRYLAVRASELIAIIGHELPIQGTYRITANAKDEQCTLRGLKVYYSKKRGEKDVDNCIYEIANGIWTQLNIFVRADWSPMAEWGSLSFYMFPNVDDLYRCHDYVMSYMYYFPQRIYWATCKDWEAKLPRVAENVCRDHMHMGHKRWFHGTEQRRHVLQDQICQKTDRYERWRNDQDQNQMQSGPCYCSSHYFCNEWGQTERFIKYEPKNQSFPRHNYLKRHMKPEEANARSESRYCEMSGQFLWLGLENSKHLVRSERWSRDKYYQKFIARIAAHDKILMINYWRATKGAMSHKRTGPQDGVCIWVCWNSKVRMQGYDCTNNACCWCPSCAAMIKENILNYTHAVNTRVWQFNYITRDYQDCWKERNIRQQPWHRFHSCLQLCCHDFIIDKTTLVDFGSLVCARLHPQCNVVYYKAQINRRFMTDCIDVTIVVWPKQEKNAFGRHHQALFPRGHYSGADCVIFDHTKILRIDLSKPHESHWWKYHLPKIAFAGHSVDDPIFIIYMCNHRVPSWAMAWWVKHLTSSMGVFRCISWCNQHLTRTIRKLMYSFGGAPSLPFQMFGINSLEVPNCVTPFIDYRSRVMSDNHSPLKVDVNIMKWQTEYFKGLWCEMTHMERIDYKLCRQFETWCCDMQHSKMPGQMPFIFVFDEMLIFQTPRPDTYENYYRIIGEMHRNYACWPIAFPHDDLPHTVVLKFANNCFRWHDQVINYFGLFVKVYACLPLWVLLLHCEWMMHRVSRMNVCGPILPCEKADILQVKSHEMFPGANGECPYWDPGSCHDAVACCFAKGGEHCGSEMMNKPANTKCHPSANSMWQRHASPRQIIAANHCIALGKERGYHPLQKKHAWRGLEPQWHKSTYKQRCCPMICADIMVDMTWDAHQWGSNFRDEPIYCWAINTHGLHHEIFCYAILHDHCGEHTMVHWVMFNIPPMQHWKVRHEHPGCRGVMDEPSLVFFSSDGSNWIKVTSEALFVDIYPQQPKGDAWEVCKQEPPEISELGSEHSANASCNNFIYSGTKTFRMDNQGECSNKAFALCFIMCIWCTYTEKYMAPRNAVLSKADCSPIWMEEILFVFMPAYYPGDIFPWMAEKDCIYAMTDNNHDDPVRCECKSEAQEQIMCMPSHFKCRSYVVKRHMSGAPETIGFAWKPCNNGTLMVLKATLAFGYSCGCYLITRSLAQHYMNIYEYIIAMDWCRGMGNEIHPVIDDSCKTRDVTIHCHKDVMWPGEMEENEGCRWVLCVIKQMQVMIFWDINTYHSVNSARIKWRGKFTCGATGHDGWKCCACDEYRIMEFLDLDWQEGGRQMFACVPANSMPFCIFLVVVGYTICHSIICDTNYGYWECPSSECIRVKKSTLYILASHISYKRTTTDLSHYFMMTYYYEFCEVLTMVQTMNSKVVRDYHAEHVQPRVNAVYGPNSYETIVGHERFLTWTCAKWWSSVWNLEMDRRFMLQLFRCEISMQMLFKVQPYYMARACNYGVGYMWEGTATVACLGKVCNVAVFKFEPFCKMLDRPTIQPDIIYNATIYIDDLDSDKICYMSICVYFYNLVSYYSAHEDFAVCIQHITWELDVFGQNDYMELVIGHI', )) def test_splc(self):