First commit

.gitignore

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+__py_cache__
+*.pyc

data/eva71.fna

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+>EVA71_BrCr_U22521 EVA71
+TTAAAACAGCTGTGGGTTGTCACCCACCCACAGGGTCCACTGGGCGCT
+AGTACACTGGTATCTCGGTACCTTTGTACGCCTGTTTTATACCCCCTCCC
+TGATTTGCAACTTAGAAGCAACGCAAACCAGATCAATAGTAGGT
+GTGACATACCAGTCGCATCTTGATCAAGCACTTCTGTATCCCCGGACCGA
+GTATCAATAGACTGTGCACACGGTTGAAGGAGAAAACGTCCGTTACCCGG
+CTAACTACTTCGAGAAGCCTAGTAACGCCATTGAAGTTGCAGAGTGTTTC
+GCTCAGCACTCCCCCCGTGTAGATCAGGTCGATGAGTCACCGCATTC
+CCCACGGGCGACCGTGGCGGTGGCTGCGTTGGCGGCCTGCCTATGGGGTA
+ACCCATAGGACGCTCTAATACGGACATGGCGTGAAGAGTCTATTGAGCTA
+GTTAGTAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACTGCGGAGCAC
+ATACCCTTAATCCAAAGGGCAGTGTGTCGTAACGGGCAACTCTGCAGCGG
+AACCGACTACTTTGGGTGTCCGTGTTTCTTTTTATTCTTGTATTGGCTGC
+TTATGGTGACAATTAAAGAATTGTTACCATATAGCTATTGGATTGGCCAT
+CCAGTGTCAAACAGAGCTATTGTATATCTCTTTGTTGGATTCACACCTCT
+CACTCTTGAAACGTTACACACCCTCAATTACATTATACTGCTGAACAC
+GAAGCGATGGGCTCCCAGGTCTCCACACAGCGATCCGGCTCGCAT
+GAGAATTCCAACTCAGCCACGGAAGGCTCCACTATAAATTACACAACCAT
+TAATTACTACAAAGACTCGTATGCTGCCACTGCTGGAAAGCAAAGTCTCA
+AACAAGATCCTGACAAGTTTGCGAACCCTGTGAAGGACATCTTTACTGAA
+ATGGCAGCGCCCTTAAAGTCTCCCTCTGCTGAAGCATGTGGCTATAGCGA
+CCGAGTGGCACAGCTTACCATTGGAAATTCCACCATTACTACACAAGAAG
+CAGCAAACATAATAGTTGGGTATGGTGAGTGGCCTTCATACTGCTCTGAT
+AATGATGCAACAGCGGTAGACAAACCTACACGGCCTGATGTCTCAGTAAA
+TAGATTTTACACGCTAGACACTAAGCTATGGGAGAAATCATCCAAGGGGT
+GGTACTGGAAGTTCCCAGATGTACTGACTGAAACCGGAGTTTTTGGTCCA
+AATGCACAATTTCACTACTTATACCGTTCAGGGTTCTGCATCCACGTTCA
+ATGTAACGCTAGCAAATTTCACCAAGGGGCGCTACTCGTTGCGGTATTGC
+CCGAGTATGTCATTGGAACAGTGGCAGGCGGCACAGGCACAGA
+GAACAGTCACCCTCCTTATAAACAAACCCAACCCGGCGCTGATGG
+ATTTGAATTACAACATCCATATGTTCTTGATGCTGGAATTCCAATATCTC
+AGTTGACAGTGTGCCCTCACCAGTGGATCAATTTACGAACCAACAATTGT
+GCCACCATAATAGTGCCATACATGAACACACTACCTTTTGATTCCGCATT
+GAACCACTGTAATTTCGGACTATTGGTGGTGCCTATCAGCCCGCTGGAT
+TTCGACCAAGGGGCGACACCGGTAATTCCTATCACTATCACGTTGGCTCC
+GATGTGTTCTGAGTTTGCGGGTCTCAGGCAGGCAGTTACGCAGGGTTTTC
+CCACTGAATTGAAACCTGGCACTAATCAGTTCTTAACCACGGATGATGGT
+GTGTCAGCACCTATATTGCCAAATTTCCACCCCACCCCGTGCATTCACAT
+ACCTGGCGAGGTTAGAAACTTACTAGAACTGTGCCAGGTAGAAACCATTT
+TAGAAGTCAACAATGTGCCCACCAACGCAACCAGTTTGATGGAAAGGCTA
+CGGTTTCCAGTGTCAGCCCAAGCAGGGAAAGGTGAGTTGTGTGCAGTGTT
+CAGGGCCGACCCTGGGAGGGATGGTCCTTGGCAATCCACCATGCTAGGCC
+AGTTGTGTGGATATTACACCCAATGGTCAGGGTCTTTGGAAGTCACTTTT
+ATGTTCACCGGATCCTTTATGGCAACTGGTAAAATGCTTATAGCTTACAC
+ACCCCCAGGGGGCCCTTTGCCTAAAGATAGAGCCACAGCTATGCTGGGGA
+CGCACGTCATCTGGGACTTTGGCTTGCAATCGTCCGTCACCCTCGTCATA
+CCATGGATCAGTAACACTCACTATAGGGCGCATGCTCGAGATGGGGTGTT
+TGATTACTACACCACAGGTTTGGTTAGTATATGGTACCAAACAAATTATG
+TAGTCCCTATTGGAGCACCTAATACTGCCTATATAATAGCGTTGGCAGCA
+GCCCAAAAGAATTTCACTATGAAATTGTGCAAGGACACCAGTGACATTTT
+GGAAACGGCCACTATTCAAGGGGACAGAGTGGCAGATGTGATTGAGAGCT
+CTATAGGAGATAGTGTGAGTAAGGCCCTCACCCCAGCTTTACCTGCACC
+CACAGGCCCAGACACCCAAGTGAGCAGTCATCGCTTAGACACTGGAAA
+AGTACCAGCACTTCAAGCCGCCGAAATCGGAGCTTCGTCGAATGCTAGTG
+ATGAGAGTATGATTGAGACTCGGTGTGTTCTTAACTCACATAGCACAGCT
+GAAACCACCCTTGATAGTTTCTTCAGCAGAGCAGGCTTAGTTGGGGAGAT
+AGATCTTCCTCTAAAGGGCACCACCAATCCGAACGGGTATGCCAACTGGG
+ACATAGACATAACCGGTTATGCGCAGATGCGCAGAAAAGTGGAACTATTC
+ACCTATATGCGCTTTGACGCAGAGTTCACTTTTGTCGCGTGCACACCTAC
+CGGAAGGGTCGTTCCACAGCTGCTTCAATACATGTTTGTTCCACCCGGGG
+CCCCCAAACCAGACTCCAGAGACTCTTTGGCTTGGCCAACGGCCACGAAC
+CCCTCAGTTTTTGTCAAATCATCCGACCCACCAGCACAAGTCTCAGTGCC
+ATTTATGTCACCTGCAAGCGCATACCAATGGTTTTATGACGGATACCCTA
+CATTTGGAGAGCACAAGCAAGAGAAGGATCTCGAGTATGGGGCATGCCCG
+AATAACATGATGGGCACATTCTCAGTGCGGACTGTGGGATCGTCAAAGTC
+AGAATATTCCTTAGTCATCAGAATATACATGAGAATGAAGCACGTCAGAG
+CGTGGATACCTCGGCCGATGCGCAATCAGAACTATTTGTTCAAATCCAAC
+CCAAACTATGCTGGTGATTCCATTAAACCAACTGGTACCAGCCGAA
+CGGCAATCACTA
+CGCTCGGGAAATTCGGTCAGCAGTCTGGGGCTATTTATGTGGGCAACTTT
+AGGGTAGTAAACAGACACCTAGCCACCCATACTGACTGGGCCAACTTGGT
+GTGGGAAGACAGCTCTAGAGACCTCCTAGTTTCTTCAACTACCGCTCAAG
+GGTGTGACACCATTGCTCGATGTAACTGCCAAACCGGAGTGTATTACTGT
+AACTCTCGCAGAAAACACTATCCAGTCAGTTTTTCGAAACCTAGTTTGGT
+GTTTGTAGAAGCTAGTGAGTATTATCCAGCTAGATATCAGTCCCATCTTA
+TGCTTGCTGAGGGCCATTCAGAACCTGGTGATTGTGGCGGTATTCTTAGA
+TGCCAACACGGTGTGGTGGGAATTGTCTCCACTGGCGGAAGTGGCCTTGT
+GGGATTTGCTGACGTTAGAGATCTTCTGTGGCTAGATGAGGAAGCGATGG
+AGCAGGGGGTATCTGATTACATCAAAGGTCTCGGTCGAGCCTTCGGCACA
+GGTTTCACTGACGCAGTGTCTAGGGAAGTGGAAGCGTTGAAGAACCACTT
+AATCGGCTCCGAAGGGGCTGTTGAGAAGATCTTGAAGAACTTGGTGAAGC
+TAATTTCAGCCTTAGTTATAGTCATCAGAAGTGATTATGATATGGTCACC
+CTCACAGCCACACTAGCTCTGATCGGGTGCCACGGGAGTCCTTGGGCGTG
+GATCAAATCAAAGACAGCTTCCATACTGGGCATTCCCATGGCACAAAAAC
+AGAGTGCCTCATGGCTAAAGAAGTTCAATGACATGGCAAATGCTGCAAAA
+GGGCTTGAGTGGATTTTCAACAAGATCAGTAAGTTCATTGACTGGCTTAA
+AGAGAAGATCATTCCAGCTGCCAAAGAGAAAGTTGAGTTTTTGAACAACC
+TAAAACAGCTCCCCTTGTTGGAGAACCAAGTCTCCAATCTTGAACAGTCT
+GCTGCCTCACAAGAAGACTTAGAAGCTATGTTTGGTAATGTGATATATCT
+GGCTCACTTTTGCCGCAAATTCCAACCACTCTACGCAACTGAGGCCAAGA
+GAGTCTACGCTTTAGAGAAAAGGATGAATAACTACATGCAGTTCAAGAGC
+AAACACCGTATTGAACCTGTATGCTTGATCATCAGAGGTTCCCCCGGAAC
+GGGCAAATCGCTCGCCACAGGCATTATAGCTAGAGCCATTGCTGACAAGT
+ATCGCTCTAGTGTATACTCACTCCCCCCAGACCCAGATCACTTTGATGGG
+TATAAGCAACAGGTGGTCGCGGTCATGGATGATCTCTGCCAGAACCCGGA
+CGGAAAAGACATGTCCCTATTTTGTCAAATGGTTTCTACAGTAGATTTTG
+TACCACCCATGGCATCACTAGAGGAGAAAGGAGTGTCCTTCACCTCTAAG
+TTTGTCATTGCATCGACCAATGCTAGTAACATCATAGTCCCCACAGTTTC
+AGATTCAGATGCAATTCGCAGGCGATTCTATATGGACTGCGATATAGAAG
+TGACAGATTCTTACAAGACAGACCTCGGTCGGCTGGACGCAGGTAGAGCT
+GCCAAGCTTTGTACAGAAAATAACACTGCTAATTTTAAGAGATGCAGCCC
+ACTGGTGTGTGGTAAGGCTATTCAGCTGAGAGACAGGAAGTCCAAAGTGA
+GATATAGCGTCGACACCGTGGTATCGGAACTGATCAGAGAGTACAACAAT
+AGATCTGCTATTGGGAATACTATAGAAGCACTCTTTCAAGGACCCCCTAA
+ATTCAGGCCTATAAGAATTAGTCTCGAAGAAAAGCCAGCCCCAGATGCCA
+TTAGCGATCTCCTCGCTAGTGTAGATAGCGAGGAGGTGCGTCAGTACTGC
+AGGGAACAAGGCTGGATCATCCCTGAAACTCCCACCAATGTTGAGCGTCA
+CCTCAATAGAGCAGTATTGGTAATGCAGTCCATCGCCACTGTGGTTGCAG
+TTGTGTCTCTTGTTTATGTCATTTATAAGCTGTTTGCCGGGTTCCAGGGT
+GCTTACTCTGGAGCGCCCAAGCCCATTCTCAAGAAGCCCGTGTTAAGAAC
+AGCCACGGTCCAAGGGCCCAGCTTAGACTTCGCCTTGTCTCTTTTGAGGC
+GCAACATTAGACAAGCGCAAACTGACCAAGGACACTTCACCATGCTAGGA
+GTGCGAGATCGCCTAGCCATCCTGCCGCGCCACTCGCAACCAGGGAAGAC
+CATCTGGGTAGAGCATAAATTAATCAATGTACTAGATGCAGTTGAGTTGG
+TGGATGAGCAAGGTGTAAACTTGGAACTCACACTGGTAACTTTGGACACC
+AATGAAAAATTTAGGGATATCACCAAGTGTATCCCAGAAGTGATCACCGG
+GGCGAGTGACGCAACTCTAGTCATCAACACTGAGCACATTCCCTCAATGT
+TTGTGCCGGTGGGTGACGTTGTGCAGTACGGTTTCTTGAACCTTAGTGGT
+AAACCCACACACAGAACCATGATGTATAACTTCCCCACGAAGCCAGGACA
+GTGTGGGGGGGTGGTTACCTCAGTTGGTAAGATCATTGGAATCCACATTG
+GCGGGAATGGACGCCAGGCCTTTTGCGCTGGCCTAAAGAGGAGTTATTTT
+GCCAGCGAGCAAGGAGAGATCCAGTGGATGAAGCCTAACAGAGAAACCGG
+GAGGTTGAATATTAATGGTCCAACCCGAACTAAGCTGGAACCCAGTGTAT
+TCCATGATGTGTTCGAGGGCAACAAGGAACCAGCGGTCCTGACTAGTAAG
+GACCCCAGACTTGAGGTTGATTTTGAGCAAGCTTTGTTCTCCAAGTATGT
+GGGTAACACCCTGCATGAACCTGATGAGTACGTGACACAGGCTGCTCTCC
+ACTACGCAAATCAGCTGAAGCAACTGGACATCAACACCAGCAAGATGAGC
+ATGGAAGAAGCGTGCTATGGCACAGAATATTTAGAAGCTATAGACTTGCA
+CACCAGTGCTGGATACCCTTATAGTGCTTTGGGCATCAAGAAAAGAGACA
+TCCTCGACCCAGTTACCAGAGACACCTCCAGGATGAAGTTATATATGGAT
+AAGTATGGGTTGGACTTGCCTAATTCCACTTATGTAAAGGATGAGCTTAG
+TTCTCTAGATAAGATCAGAAAAGGGGAGTCTCGCCTGATTGAGGCTAGCA
+GCTTAAATGATCCTGTCTACCCTAGATTGACTTTTGGACACCTTTATGAA
+GTGTTTCACGCCAACCCAGGGACTGTAACAGGATCTGCAGTTGGGTGCAA
+CCCTGATGTATTTTGGAGCAAGTTACCAATTTTGTTACCGGGTTCACTCT
+TTGCATTTGACTACTCAGGATATGATGCAAGCCTTAGTCCTGTGTGGTTC
+AGAGCTCTAGAGTTGGTTCTGAGAGAGATCGGTTACTCGGAGGAGGCTGT
+GTCACTCATAGAAGGGATCAATCACACCCACCACGTGTACCGAAACAAGA
+CATATTGTGTACTTGGTGGAATGCCCTCAGGCTGCTCCGGTACTTCCATT
+TTCAATTCCATGATTAACAACATAATCATCAGAACCCTCCTGATTAAAAC
+ATTCAAAGGTATAGACTTAGATGAGCTGAAAATGGTAGCTTATGGAGATG
+ACGTGTTGGCCAGCTACCCGTTTCCTATTGATTGCTTGGAATGGGGTAAA
+ACAGGCAAAGAATATGGGCTGACTATGACTCCTGCTGATAAATCACCTTG
+TTTCAATGAGGTTACCTGGGAGAATGCAACCTTCTTAAAACGGGGTTTTC
+TACCGGACCATCAGTTCCCTTTTCTGATCCATCCCACTATGCCCATGAGG
+GAAATCCATGAGTCCATCCGCTGGACCAAGGACGCGCGCAATACTCAAGA
+TCATGTGCGCTCCCTTTGTCTCCTGGCATGGCATAATGGAAAAGAGGAGT
+ATGAGAAATTTGTGAGTACAATTAGATCAGTCCCCATTGGAAGGGCTTTA
+GCAATTCCAAATTTGGAGAACTTGAGAAGAAATTGGCTCGAGTTATTTTA
+AACTTACAGCTCAATGCTGAACCCCACCAGAAATCTGGTCGTGTCAAT
+GACTGGTGGGGGTAAATTTGTTATAACCAGAATAGC

tests/context.py

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+import os
+import sys
+# Path of debruijn package
+#sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__),
+#                                                '..')))
+# Path for core
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                                '../debruijn')))
+import debruijn

tests/kmer.pck

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+(dp0
+S'GAG'
+p1
+I1
+sS'CAG'
+p2
+I1
+sS'AGA'
+p3
+I2
+sS'TCA'
+p4
+I1
+s.

tests/test_build.fq

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+@EVA71_BrCr_U22521-1480
+TCAGAGA
++
+JJJJJJJ

tests/test_construction_debruijn.py

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+"""Tests for graph build"""
+import pytest
+import os
+import networkx as nx
+import pickle
+from .context import debruijn
+from debruijn import read_fastq
+from debruijn import cut_kmer
+from debruijn import build_kmer_dict
+from debruijn import build_graph
+
+
+def test_read_fastq():
+    """Test fastq reading"""
+    fastq_reader = read_fastq(os.path.abspath(os.path.join(os.path.dirname(__file__), "test_two_reads.fq")))
+    assert next(fastq_reader) == "TCAGAGCTCTAGAGTTGGTTCTGAGAGAGATCGGTTACTCGGAGGAGGCTGTGTCACTCATAGAAGGGATCAATCACACCCACCACGTGTACCGAAACAA"
+    assert next(fastq_reader) == "TTTGAATTACAACATCCATATGTTCTTGATGCTGGAATTCCAATATCTCAGTTGACAGTGTGCCCTCACCAGTGGATCAATTTACGAACCAACAATTGTG"
+
+
+def test_cut_kmer():
+    """test Kmer cut"""
+    kmer_reader = cut_kmer("TCAGA", 3)
+    assert next(kmer_reader) == "TCA"
+    assert next(kmer_reader) == "CAG"
+    assert next(kmer_reader) == "AGA"
+
+
+def test_build_kmer_dict():
+    kmer_dict = build_kmer_dict(os.path.abspath(os.path.join(os.path.dirname(__file__), "test_build.fq")), 3)
+    assert(len(kmer_dict.keys()) == 4)
+    assert "TCA" in kmer_dict
+    assert "CAG" in kmer_dict
+    assert "AGA" in kmer_dict
+    assert "GAG" in kmer_dict
+    assert kmer_dict["AGA"] == 2
+
+def test_build_graph():
+    file = open(os.path.abspath(os.path.join(os.path.dirname(__file__), "kmer.pck")),'rb')
+    kmer_dict = pickle.load(file)
+    graph = build_graph(kmer_dict)
+    #TCAGAGA
+    #TCA  TC CA
+    #CAG CA AG
+    #AGA AG GA
+    #GAG GA AG
+    #AGA AG GA
+    assert graph.number_of_nodes() == 4
+    assert graph.number_of_edges() == 4
+    assert "AG" in graph
+    assert "GA" in graph
+    assert graph.edges["AG", "GA"]['weight'] == 2

tests/test_two_reads.fq

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+@EVA71_BrCr_U22521-1480
+TCAGAGCTCTAGAGTTGGTTCTGAGAGAGATCGGTTACTCGGAGGAGGCTGTGTCACTCATAGAAGGGATCAATCACACCCACCACGTGTACCGAAACAA
++
+JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
+@EVA71_BrCr_U22521-1478
+TTTGAATTACAACATCCATATGTTCTTGATGCTGGAATTCCAATATCTCAGTTGACAGTGTGCCCTCACCAGTGGATCAATTTACGAACCAACAATTGTG
++
+JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ