SYMBOL INDEX (425 symbols across 30 files)

FILE: pyGeno/Chromosome.py
  class ChrosomeSequence (line 20) | class ChrosomeSequence(object) :
    method __init__ (line 23) | def __init__(self, data, chromosome, refOnly = False) :
    method setSNPFilter (line 30) | def setSNPFilter(self, SNPFilter) :
    method getSequenceData (line 33) | def getSequenceData(self, slic) :
    method _getSequence (line 88) | def _getSequence(self, slic) :
    method __getitem__ (line 91) | def __getitem__(self, i) :
    method __len__ (line 94) | def __len__(self) :
  class Chromosome_Raba (line 97) | class Chromosome_Raba(pyGenoRabaObject) :
    method _curate (line 110) | def _curate(self) :
  class Chromosome (line 116) | class Chromosome(pyGenoRabaObjectWrapper) :
    method __init__ (line 121) | def __init__(self, *args, **kwargs) :
    method getSequenceData (line 134) | def getSequenceData(self, slic) :
    method _makeLoadQuery (line 137) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method __getitem__ (line 154) | def __getitem__(self, i) :
    method __str__ (line 157) | def __str__(self) :

FILE: pyGeno/Exon.py
  class Exon_Raba (line 8) | class Exon_Raba(pyGenoRabaObject) :
    method _curate (line 30) | def _curate(self) :
  class Exon (line 49) | class Exon(pyGenoRabaObjectWrapper) :
    method __init__ (line 54) | def __init__(self, *args, **kwargs) :
    method _makeLoadQuery (line 58) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method _load_data (line 77) | def _load_data(self) :
    method _load_bin_sequence (line 106) | def _load_bin_sequence(self) :
    method hasCDS (line 112) | def hasCDS(self) :
    method getCDSLength (line 118) | def getCDSLength(self) :
    method find (line 122) | def find(self, sequence) :
    method findAll (line 126) | def findAll(self, sequence):
    method findInCDS (line 130) | def findInCDS(self, sequence) :
    method findAllInCDS (line 134) | def findAllInCDS(self, sequence):
    method pluck (line 138) | def pluck(self) :
    method nextExon (line 145) | def nextExon(self) :
    method previousExon (line 152) | def previousExon(self) :
    method __str__ (line 163) | def __str__(self) :
    method __len__ (line 166) | def __len__(self) :

FILE: pyGeno/Gene.py
  class Gene_Raba (line 8) | class Gene_Raba(pyGenoRabaObject) :
    method _curate (line 24) | def _curate(self) :
  class Gene (line 27) | class Gene(pyGenoRabaObjectWrapper) :
    method __init__ (line 32) | def __init__(self, *args, **kwargs) :
    method _makeLoadQuery (line 35) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method __str__ (line 54) | def __str__(self) :

FILE: pyGeno/Genome.py
  function getGenomeList (line 16) | def getGenomeList() :
  class Genome_Raba (line 25) | class Genome_Raba(pyGenoRabaObject) :
    method _curate (line 37) | def _curate(self) :
    method getSequencePath (line 40) | def getSequencePath(self) :
    method getReferenceSequencePath (line 43) | def getReferenceSequencePath(self) :
    method __len__ (line 46) | def __len__(self) :
  class Genome (line 54) | class Genome(pyGenoRabaObjectWrapper) :
    method __init__ (line 65) | def __init__(self, SNPs = None, SNPFilter = None,  *args, **kwargs) :
    method _makeLoadQuery (line 99) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method __str__ (line 116) | def __str__(self) :

FILE: pyGeno/Protein.py
  class Protein_Raba (line 12) | class Protein_Raba(pyGenoRabaObject) :
    method _curate (line 25) | def _curate(self) :
  class Protein (line 29) | class Protein(pyGenoRabaObjectWrapper) :
    method __init__ (line 34) | def __init__(self, *args, **kwargs) :
    method _makeLoadQuery (line 38) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method _load_sequences (line 57) | def _load_sequences(self) :
    method getSequence (line 64) | def getSequence(self):
    method _load_bin_sequence (line 67) | def _load_bin_sequence(self) :
    method getDefaultSequence (line 70) | def getDefaultSequence(self) :
    method getPolymorphisms (line 74) | def getPolymorphisms(self) :
    method find (line 78) | def find(self, sequence):
    method findAll (line 82) | def findAll(self, sequence):
    method findString (line 86) | def findString(self, sequence) :
    method findStringAll (line 90) | def findStringAll(self, sequence):
    method __getitem__ (line 94) | def __getitem__(self, i) :
    method __len__ (line 97) | def __len__(self) :
    method __str__ (line 100) | def __str__(self) :

FILE: pyGeno/SNP.py
  function getSNPSetsList (line 18) | def getSNPSetsList() :
  class SNPMaster (line 27) | class SNPMaster(Raba) :
    method _curate (line 35) | def _curate(self) :
  class SNP_INDEL (line 39) | class SNP_INDEL(Raba) :
    method __init__ (line 56) | def __init__(self, *args, **kwargs) :
    method __getattribute__ (line 59) | def __getattribute__(self, k) :
    method __setattr__ (line 66) | def __setattr__(self, k, v) :
    method _curate (line 73) | def _curate(self) :
    method ensureGlobalIndex (line 77) | def ensureGlobalIndex(cls, fields) :
    method __repr__ (line 80) | def __repr__(self) :
  class CasavaSNP (line 83) | class CasavaSNP(SNP_INDEL) :
  class AgnosticSNP (line 101) | class AgnosticSNP(SNP_INDEL) :
    method __repr__ (line 122) | def __repr__(self) :
  class dbSNPSNP (line 125) | class dbSNPSNP(SNP_INDEL) :
  class TopHatSNP (line 198) | class TopHatSNP(SNP_INDEL) :

FILE: pyGeno/SNPFiltering.py
  class Sequence_modifiers (line 7) | class Sequence_modifiers(object) :
    method __init__ (line 9) | def __init__(self, sources = {}) :
    method addSource (line 12) | def addSource(self, name, snp) :
  class SequenceSNP (line 16) | class SequenceSNP(Sequence_modifiers) :
    method __init__ (line 18) | def __init__(self, alleles, sources = {}) :
  class SequenceInsert (line 25) | class SequenceInsert(Sequence_modifiers) :
    method __init__ (line 28) | def __init__(self, bases, sources = {}, ref = '-') :
  class SequenceDel (line 44) | class SequenceDel(Sequence_modifiers) :
    method __init__ (line 46) | def __init__(self, length, sources = {}, ref = None, alt = '-') :
  class SNPFilter (line 64) | class SNPFilter(object) :
    method __init__ (line 67) | def __init__(self) :
    method filter (line 70) | def filter(self, chromosome, **kwargs) :
  class DefaultSNPFilter (line 73) | class DefaultSNPFilter(SNPFilter) :
    method __init__ (line 102) | def __init__(self) :
    method filter (line 105) | def filter(self, chromosome, **kwargs) :

FILE: pyGeno/Transcript.py
  class Transcript_Raba (line 14) | class Transcript_Raba(pyGenoRabaObject) :
    method _curate (line 34) | def _curate(self) :
  class Transcript (line 52) | class Transcript(pyGenoRabaObjectWrapper) :
    method __init__ (line 57) | def __init__(self, *args, **kwargs) :
    method _makeLoadQuery (line 63) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method _load_data (line 83) | def _load_data(self) :
    method _load_bin_sequence (line 151) | def _load_bin_sequence(self) :
    method getNucleotideCodon (line 157) | def getNucleotideCodon(self, cdnaX1) :
    method getCodon (line 161) | def getCodon(self, i) :
    method iterCodons (line 165) | def iterCodons(self) :
    method find (line 170) | def find(self, sequence) :
    method findAll (line 174) | def findAll(self, sequence):
    method findIncDNA (line 178) | def findIncDNA(self, sequence) :
    method findAllIncDNA (line 182) | def findAllIncDNA(self, sequence) :
    method getcDNALength (line 186) | def getcDNALength(self) :
    method findInUTR5 (line 190) | def findInUTR5(self, sequence) :
    method findAllInUTR5 (line 194) | def findAllInUTR5(self, sequence) :
    method getUTR5Length (line 198) | def getUTR5Length(self) :
    method findInUTR3 (line 202) | def findInUTR3(self, sequence) :
    method findAllInUTR3 (line 206) | def findAllInUTR3(self, sequence) :
    method getUTR3Length (line 210) | def getUTR3Length(self) :
    method getNbCodons (line 214) | def getNbCodons(self) :
    method __getattribute__ (line 218) | def __getattribute__(self, name) :
    method __getitem__ (line 221) | def __getitem__(self, i) :
    method __len__ (line 224) | def __len__(self) :
    method __str__ (line 227) | def __str__(self) :

FILE: pyGeno/bootstrap.py
  function listRemoteDatawraps (line 11) | def listRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
  function printRemoteDatawraps (line 19) | def printRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
  function _DW (line 49) | def _DW(name, url) :
  function importRemoteGenome (line 58) | def importRemoteGenome(name, batchSize = 100) :
  function importRemoteSNPs (line 68) | def importRemoteSNPs(name) :
  function listDatawraps (line 78) | def listDatawraps() :
  function printDatawraps (line 91) | def printDatawraps() :
  function importGenome (line 102) | def importGenome(name, batchSize = 100) :
  function importSNPs (line 107) | def importSNPs(name) :

FILE: pyGeno/configuration.py
  class PythonVersionError (line 6) | class PythonVersionError(Exception) :
  function version (line 28) | def version() :
  function prettyVersion (line 32) | def prettyVersion() :
  function checkPythonVersion (line 36) | def checkPythonVersion() :
  function getGenomeSequencePath (line 43) | def getGenomeSequencePath(specie, name) :
  function createDefaultConfigFile (line 46) | def createDefaultConfigFile() :
  function getSettingsPath (line 53) | def getSettingsPath() :
  function removeFromDBRegistery (line 63) | def removeFromDBRegistery(obj) :
  function freeDBRegistery (line 68) | def freeDBRegistery() :
  function reload (line 72) | def reload() :
  function pyGeno_init (line 76) | def pyGeno_init() :

FILE: pyGeno/examples/snps_queries.py
  function printing (line 10) | def printing(gene) :
  function printVs (line 23) | def printVs(refGene, presGene) :
  function fancyExonQuery (line 35) | def fancyExonQuery(gene) :
  class QMax_gt_filter (line 39) | class QMax_gt_filter(SNPFilter) :
    method __init__ (line 41) | def __init__(self, threshold) :
    method filter (line 44) | def filter(self, chromosome, dummySRY) :

FILE: pyGeno/importation/Genomes.py
  function backUpDB (line 22) | def backUpDB() :
  function _decompressPackage (line 30) | def _decompressPackage(packageFile) :
  function _getFile (line 43) | def _getFile(fil, directory) :
  function deleteGenome (line 58) | def deleteGenome(species, name) :
  function importGenome (line 99) | def importGenome(packageFile, batchSize = 50, verbose = 0) :
  function _importGenomeObjects (line 201) | def _importGenomeObjects(gtfFilePath, chroSet, genome, batchSize, verbos...
  function _importSequence (line 445) | def _importSequence(chromosome, fastaFile, targetDir) :

FILE: pyGeno/importation/SNPs.py
  function importSNPs (line 14) | def importSNPs(packageFile) :
  function deleteSNPs (line 86) | def deleteSNPs(setName) :
  function _importSNPs_AgnosticSNP (line 102) | def _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile) :
  function _importSNPs_CasavaSNP (line 150) | def _importSNPs_CasavaSNP(setName, species, genomeSource, snpsFile) :
  function _importSNPs_dbSNPSNP (line 197) | def _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) :
  function _importSNPs_TopHatSNP (line 236) | def _importSNPs_TopHatSNP(setName, species, genomeSource, snpsFile) :

FILE: pyGeno/pyGenoObjectBases.py
  function nosave (line 7) | def nosave() :
  class pyGenoRabaObject (line 10) | class pyGenoRabaObject(Raba) :
    method __init__ (line 23) | def __init__(self) :
    method _curate (line 27) | def _curate(self) :
    method save (line 31) | def save(self) :
  class pyGenoRabaObjectWrapper_metaclass (line 39) | class pyGenoRabaObjectWrapper_metaclass(type) :
    method __new__ (line 44) | def __new__(cls, name, bases, dct) :
  class RLWrapper (line 49) | class RLWrapper(object) :
    method __init__ (line 51) | def __init__(self, rabaObj, listObjectType, rl) :
    method __getitem__ (line 56) | def __getitem__(self, i) :
    method __getattr__ (line 59) | def __getattr__(self, name) :
  class pyGenoRabaObjectWrapper (line 63) | class pyGenoRabaObjectWrapper(object) :
    method __init__ (line 73) | def __init__(self, wrapped_object_and_bag = (), *args, **kwargs) :
    method _getObjBagKey (line 92) | def _getObjBagKey(self, obj) :
    method _makeLoadQuery (line 98) | def _makeLoadQuery(self, objectType, *args, **coolArgs) :
    method count (line 112) | def count(self, objectType, *args, **coolArgs) :
    method get (line 116) | def get(self, objectType, *args, **coolArgs) :
    method iterGet (line 137) | def iterGet(self, objectType, *args, **coolArgs) :
    method __getattr__ (line 164) | def __getattr__(self, name) :
    method getIndexes (line 200) | def getIndexes(cls) :
    method flushIndexes (line 206) | def flushIndexes(cls) :
    method help (line 212) | def help(cls) :
    method ensureGlobalIndex (line 218) | def ensureGlobalIndex(cls, fields) :
    method dropGlobalIndex (line 226) | def dropGlobalIndex(cls, fields) :
    method getSequencesData (line 230) | def getSequencesData(self) :
    method _load_sequences (line 235) | def _load_sequences(self) :
    method _load_data (line 240) | def _load_data(self) :
    method _load_bin_sequence (line 245) | def _load_bin_sequence(self) :

FILE: pyGeno/tests/test_csv.py
  class CSVTests (line 4) | class CSVTests(unittest.TestCase):
    method setUp (line 6) | def setUp(self):
    method tearDown (line 9) | def tearDown(self):
    method test_createParse (line 12) | def test_createParse(self) :
  function runTests (line 28) | def runTests() :

FILE: pyGeno/tests/test_genome.py
  class pyGenoSNPTests (line 8) | class pyGenoSNPTests(unittest.TestCase):
    method setUp (line 10) | def setUp(self):
    method tearDown (line 33) | def tearDown(self):
    method test_vanilla (line 37) | def test_vanilla(self) :
    method test_noModif (line 46) | def test_noModif(self) :
    method test_insert (line 63) | def test_insert(self) :
    method test_SNP (line 83) | def test_SNP(self) :
    method test_deletion (line 103) | def test_deletion(self) :
    method test_indels (line 123) | def test_indels(self) :
    method test_bags (line 143) | def test_bags(self) :
    method test_prot_find (line 148) | def test_prot_find(self) :
    method test_trans_find (line 156) | def test_trans_find(self) :
  function runTests (line 168) | def runTests() :

FILE: pyGeno/tools/BinarySequence.py
  class BinarySequence (line 4) | class BinarySequence :
    method __init__ (line 10) | def __init__(self, sequence, arrayForma, charToBinDict) :
    method encode (line 21) | def encode(self, sequence):
    method __testFind (line 63) | def __testFind(self, arr) :
    method __testBinary (line 69) | def __testBinary(self, arr) :
    method findPolymorphisms (line 75) | def findPolymorphisms(self, strSeq, strict = False):
    method getPolymorphisms (line 96) | def getPolymorphisms(self):
    method getDefaultSequence (line 100) | def getDefaultSequence(self) :
    method __getSequenceVariants (line 104) | def __getSequenceVariants(self, x1, polyStart, polyStop, listSequence) :
    method getSequenceVariants (line 121) | def getSequenceVariants(self, x1 = 0, x2 = -1, maxVariantNumber = 128) :
    method getNbVariants (line 152) | def getNbVariants(self, x1, x2 = -1) :
    method _dichFind (line 166) | def _dichFind(self, needle, currHaystack, offset, lst = None) :
    method _kmp_construct_next (line 197) | def _kmp_construct_next(self, pattern):
    method _kmp_search_first (line 209) | def _kmp_search_first(self, pInput_sequence, pPattern):
    method _kmp_search_all (line 221) | def _kmp_search_all(self, pInput_sequence, pPattern):
    method _kmp_find (line 236) | def _kmp_find(self, needle, haystack, lst = None):
    method findByBiSearch (line 241) | def findByBiSearch(self, strSeq) :
    method findAllByBiSearch (line 246) | def findAllByBiSearch(self, strSeq) :
    method find (line 253) | def find(self, strSeq) :
    method findAll (line 258) | def findAll(self, strSeq) :
    method __and__ (line 265) | def __and__(self, arr) :
    method __xor__ (line 274) | def __xor__(self, arr) :
    method __eq__ (line 283) | def __eq__(self, seq) :
    method append (line 292) | def append(self, arr) :
    method extend (line 295) | def extend(self, arr) :
    method decode (line 298) | def decode(self, binSequence):
    method getChar (line 317) | def getChar(self, i):
    method __len__ (line 320) | def __len__(self):
    method __getitem__ (line 323) | def __getitem__(self,i):
    method __setitem__ (line 326) | def __setitem__(self, i, v):
  class AABinarySequence (line 329) | class AABinarySequence(BinarySequence) :
    method __init__ (line 332) | def __init__(self, sequence):
  class NucBinarySequence (line 337) | class NucBinarySequence(BinarySequence) :
    method __init__ (line 340) | def __init__(self, sequence):
  function test0 (line 357) | def test0() :
  function testVariants (line 377) | def testVariants() :
  function testFind (line 395) | def testFind():
  function testFindByBiSearch (line 399) | def testFindByBiSearch():
  function testFindAll (line 403) | def testFindAll():
  function testFindAllByBiSearch (line 407) | def testFindAllByBiSearch():

FILE: pyGeno/tools/ProgressBar.py
  class ProgressBar (line 3) | class ProgressBar :
    method __init__ (line 15) | def __init__(self, nbEpochs = -1, width = 25, label = "progress", minR...
    method formatTime (line 39) | def formatTime(self, val) :
    method _update (line 47) | def _update(self) :
    method log (line 60) | def log(self) :
    method saveLogs (line 68) | def saveLogs(self, filename) :
    method update (line 74) | def update(self, label = '', forceRefresh = False, log = False) :
    method close (line 116) | def close(self) :

FILE: pyGeno/tools/SecureMmap.py
  class SecureMmap (line 3) | class SecureMmap:
    method __init__ (line 6) | def __init__(self, filename, enableWrite = False) :
    method forceSet (line 15) | def forceSet(self, x1, v) :
    method __getitem__ (line 19) | def __getitem__(self, i):
    method __setitem__ (line 22) | def __setitem__(self, i, v) :
    method __str__ (line 28) | def __str__(self) :
    method __len__ (line 31) | def __len__(self) :

FILE: pyGeno/tools/SegmentTree.py
  function aux_insertTree (line 3) | def aux_insertTree(childTree, parentTree):
  function aux_moveTree (line 11) | def aux_moveTree(offset, tree):
  class SegmentTree (line 19) | class SegmentTree :
    method __init__ (line 56) | def __init__(self, x1 = None, x2 = None, name = '', referedObject = []...
    method __addChild (line 70) | def __addChild(self, segmentTree, index = -1) :
    method insert (line 77) | def insert(self, x1, x2, name = '', referedObject = []) :
    method insertTree (line 133) | def insertTree(self, childTree):
    method intersect (line 141) | def intersect(self, x1, x2 = None) :
    method __dichotomicSearch (line 179) | def __dichotomicSearch(self, x1) :
    method __radiateDown (line 196) | def __radiateDown(self, x1, x2, childId, condition) :
    method __radiateUp (line 208) | def __radiateUp(self, x1, x2, childId, condition) :
    method emptyChildren (line 220) | def emptyChildren(self) :
    method removeGaps (line 224) | def removeGaps(self) :
    method getX1 (line 231) | def getX1(self) :
    method getX2 (line 237) | def getX2(self) :
    method getIndexedLength (line 243) | def getIndexedLength(self) :
    method getFirstLevel (line 256) | def getFirstLevel(self) :
    method flatten (line 269) | def flatten(self) :
    method move (line 302) | def move(self, newX1) :
    method __str__ (line 311) | def __str__(self) :
    method __str (line 323) | def __str(self) :
    method __len__ (line 333) | def __len__(self) :
    method __repr__ (line 340) | def __repr__(self):

FILE: pyGeno/tools/SingletonManager.py
  function add (line 4) | def add(obj, objName='') :
  function contains (line 16) | def contains(k) :
  function get (line 19) | def get(objName) :

FILE: pyGeno/tools/Stats.py
  function kullback_leibler (line 3) | def kullback_leibler(p, q) :
  function squaredError_log10 (line 13) | def squaredError_log10(p, q) :
  function fisherExactTest (line 22) | def fisherExactTest(table) :

FILE: pyGeno/tools/UsefulFunctions.py
  class UnknownNucleotide (line 3) | class UnknownNucleotide(Exception) :
    method __init__ (line 4) | def __init__(self, nuc) :
    method __str__ (line 7) | def __str__(self) :
  function saveResults (line 11) | def saveResults(directoryName, fileName, strResults, log = '', args = ''):
  function findAll (line 136) | def findAll(haystack, needle) :
  function complementTab (line 153) | def complementTab(seq=[]):
  function reverseComplementTab (line 176) | def reverseComplementTab(seq):
  function reverseComplement (line 182) | def reverseComplement(seq):
  function complement (line 188) | def complement(seq) :
  function translateDNA_6Frames (line 196) | def translateDNA_6Frames(sequence) :
  function translateDNA (line 210) | def translateDNA(sequence, frame = 'f1', translTable_id='default') :
  function getSequenceCombinaisons (line 252) | def getSequenceCombinaisons(polymorphipolymorphicDnaSeqSeq, pos = 0) :
  function polymorphicCodonCombinaisons (line 276) | def polymorphicCodonCombinaisons(codon) :
  function encodePolymorphicNucleotide (line 280) | def encodePolymorphicNucleotide(polySeq) :
  function decodePolymorphicNucleotide (line 333) | def decodePolymorphicNucleotide(nuc) :
  function decodePolymorphicNucleotide_str (line 343) | def decodePolymorphicNucleotide_str(nuc) :
  function getNucleotideCodon (line 348) | def getNucleotideCodon(sequence, x1) :
  function showDifferences (line 363) | def showDifferences(seq1, seq2) :
  function highlightSubsequence (line 392) | def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') :

FILE: pyGeno/tools/io.py
  function printf (line 3) | def printf(*s) :
  function enterConfirm_prompt (line 11) | def enterConfirm_prompt(enterMsg) :
  function confirm_prompt (line 30) | def confirm_prompt(preMsg) :

FILE: pyGeno/tools/parsers/CSVTools.py
  class EmptyLine (line 3) | class EmptyLine(Exception) :
    method __init__ (line 6) | def __init__(self, lineNumber) :
    method __str__ (line 11) | def __str__(self) :
  function removeDuplicates (line 14) | def removeDuplicates(inFileName, outFileName) :
  function catCSVs (line 36) | def catCSVs(folder, ouputFileName, removeDups = False) :
  function joinCSVs (line 44) | def joinCSVs(csvFilePaths, column, ouputFileName, separator = ',') :
  class CSVEntry (line 78) | class CSVEntry(object) :
    method __init__ (line 81) | def __init__(self, csvFile, lineNumber = None) :
    method commit (line 124) | def commit(self) :
    method __iter__ (line 128) | def __iter__(self) :
    method next (line 132) | def next(self) :
    method __getitem__ (line 141) | def __getitem__(self, key) :
    method __setitem__ (line 150) | def __setitem__(self, key, value) :
    method toStr (line 166) | def toStr(self) :
    method __repr__ (line 169) | def __repr__(self) :
    method __str__ (line 176) | def __str__(self) :
  class CSVFile (line 179) | class CSVFile(object) :
    method __init__ (line 201) | def __init__(self, legend = [], separator = ',', lineSeparator = '\n') :
    method addField (line 221) | def addField(self, field) :
    method parse (line 231) | def parse(self, filePath, skipLines=0, separator = ',', stringSeparato...
    method streamToFile (line 278) | def streamToFile(self, filename, keepInMemory = False, writeRate = 1) :
    method commitLine (line 299) | def commitLine(self, line) :
    method closeStreamToFile (line 312) | def closeStreamToFile(self) :
    method _developLine (line 327) | def _developLine(self, line) :
    method get (line 342) | def get(self, line, key) :
    method set (line 346) | def set(self, line, key, val) :
    method newLine (line 350) | def newLine(self) :
    method insertLine (line 357) | def insertLine(self, i) :
    method save (line 362) | def save(self, filePath) :
    method toStr (line 370) | def toStr(self) :
    method __iter__ (line 377) | def __iter__(self) :
    method next (line 381) | def next(self) :
    method __getitem__ (line 389) | def __getitem__(self, line) :
    method __len__ (line 413) | def __len__(self) :

FILE: pyGeno/tools/parsers/CasavaTools.py
  class SNPsTxtEntry (line 4) | class SNPsTxtEntry(object) :
    method __init__ (line 7) | def __init__(self, lineNumber, snpsTxtFile) :
    method __getitem__ (line 30) | def __getitem__(self, fieldName):
    method __setitem__ (line 34) | def __setitem__(self, fieldName, value) :
    method __str__ (line 38) | def __str__(self):
  class SNPsTxtFile (line 41) | class SNPsTxtFile(object) :
    method __init__ (line 50) | def __init__(self, fil, gziped = False) :
    method reset (line 63) | def reset(self) :
    method __iter__ (line 68) | def __iter__(self) :
    method next (line 72) | def next(self) :
    method __getitem__ (line 79) | def __getitem__(self, i) :
    method __len__ (line 84) | def __len__(self) :

FILE: pyGeno/tools/parsers/FastaTools.py
  class FastaFile (line 3) | class FastaFile(object) :
    method __init__ (line 18) | def __init__(self, fil = None) :
    method reset (line 23) | def reset(self) :
    method parseStr (line 28) | def parseStr(self, st) :
    method parseFile (line 32) | def parseFile(self, fil) :
    method __splitLine (line 38) | def __splitLine(self, li) :
    method get (line 47) | def get(self, i) :
    method add (line 52) | def add(self, header, data) :
    method save (line 59) | def save(self, filePath) :
    method toStr (line 65) | def toStr(self) :
    method __iter__ (line 73) | def __iter__(self) :
    method next (line 77) | def next(self) :
    method __getitem__ (line 87) | def __getitem__(self, i) :
    method __setitem__ (line 91) | def __setitem__(self, i, v) :
    method __len__ (line 98) | def __len__(self) :

FILE: pyGeno/tools/parsers/FastqTools.py
  class FastqEntry (line 3) | class FastqEntry(object) :
    method __init__ (line 6) | def __init__(self, ident = "", seq = "", plus = "", qual = "") :
    method __getitem__ (line 13) | def __getitem__(self, i):
    method __setitem__ (line 16) | def __setitem__(self, i, v) :
    method __str__ (line 19) | def __str__(self):
  class FastqFile (line 22) | class FastqFile(object) :
    method __init__ (line 41) | def __init__(self, fil = None) :
    method reset (line 46) | def reset(self) :
    method parseStr (line 51) | def parseStr(self, st) :
    method parseFile (line 57) | def parseFile(self, fil) :
    method __splitEntry (line 63) | def __splitEntry(self, li) :
    method get (line 70) | def get(self, li) :
    method newEntry (line 76) | def newEntry(self, ident = "", seq = "", plus = "", qual = "") :
    method add (line 82) | def add(self, fastqEntry) :
    method save (line 86) | def save(self, filePath) :
    method toStr (line 91) | def toStr(self) :
    method __iter__ (line 98) | def __iter__(self) :
    method next (line 102) | def next(self) :
    method __getitem__ (line 112) | def __getitem__(self, i) :
    method __setitem__ (line 116) | def __setitem__(self, i, v) :
    method __len__ (line 123) | def __len__(self) :

FILE: pyGeno/tools/parsers/GTFTools.py
  class GTFEntry (line 3) | class GTFEntry(object) :
    method __init__ (line 4) | def __init__(self, gtfFile, lineNumber) :
    method __getitem__ (line 17) | def __getitem__(self, k) :
    method __repr__ (line 27) | def __repr__(self) :
    method __str__ (line 30) | def __str__(self) :
  class GTFFile (line 33) | class GTFFile(object) :
    method __init__ (line 35) | def __init__(self, filename, gziped = False) :
    method get (line 53) | def get(self, line, elmt) :
    method __iter__ (line 57) | def __iter__(self) :
    method next (line 61) | def next(self) :
    method __getitem__ (line 68) | def __getitem__(self, i) :
    method __repr__ (line 74) | def __repr__(self) :
    method __str__ (line 77) | def __str__(self) :
    method __len__ (line 80) | def __len__(self) :

FILE: pyGeno/tools/parsers/VCFTools.py
  class VCFEntry (line 3) | class VCFEntry(object) :
    method __init__ (line 6) | def __init__(self, vcfFile, line, lineNumber) :
    method __getitem__ (line 48) | def __getitem__(self, key) :
    method __repr__ (line 65) | def __repr__(self) :
    method __str__ (line 68) | def __str__(self) :
  class VCFFile (line 71) | class VCFFile(object) :
    method __init__ (line 83) | def __init__(self, filename = None, gziped = False, stream = False) :
    method parse (line 91) | def parse(self, filename, gziped = False, stream = False) :
    method close (line 144) | def close(self) :
    method _developLine (line 148) | def _developLine(self, lineNumber) :
    method __iter__ (line 152) | def __iter__(self) :
    method next (line 156) | def next(self) :
    method __getitem__ (line 173) | def __getitem__(self, line) :
    method __len__ (line 182) | def __len__(self) :
    method __repr__ (line 186) | def __repr__(self) :
    method __str__ (line 189) | def __str__(self) :