Contents¶
Manual
- Manual
- The
AlignandContainerclasses - Computing diversity statistics
- The
stats.ComputeStatsclass - Computing statistics
- Structure and group labels
- Missing data
- Linkage disequilibrium statistics
- Using VCF files
- The
- Coalescent simulations
- Integration of external software
- The
Statistics
History
Licence
Authors
Reference Manual
- EggLib Reference Manual
- Top level components
- Holding multi-site data
- Holding single-site data
- Representing data with alphabets
- Describing sample structure
- Trees
- Module content documentation
AlignAlign.add_label()Align.add_sample()Align.add_samples()Align.alphabetAlign.clear()Align.column()Align.consensus()Align.create()Align.del_columns()Align.del_sample()Align.encode()Align.extract()Align.fasta()Align.filter()Align.find()Align.find_motif()Align.fix_ends()Align.get()Align.get_label()Align.get_name()Align.get_sample()Align.get_sequence()Align.group_mapping()Align.insert_columns()Align.intersperse()Align.is_matrixAlign.iter_sites()Align.lower()Align.lsAlign.name_mapping()Align.names()Align.nexus()Align.nsAlign.phylip()Align.phyml()Align.random_missing()Align.remove_duplicates()Align.rename()Align.reserve()Align.reset()Align.set()Align.set_label()Align.set_name()Align.set_sample()Align.set_sequence()Align.slider()Align.subset()Align.to_bases()Align.to_codons()Align.upper()
ContainerContainer.add_label()Container.add_sample()Container.add_samples()Container.alphabetContainer.clear()Container.create()Container.del_sample()Container.del_sites()Container.encode()Container.equalize()Container.fasta()Container.find()Container.find_motif()Container.get()Container.get_label()Container.get_name()Container.get_sample()Container.get_sequence()Container.group_mapping()Container.insert_sites()Container.is_matrixContainer.lower()Container.ls()Container.name_mapping()Container.names()Container.nsContainer.remove_duplicates()Container.rename()Container.reserve()Container.reset()Container.set()Container.set_label()Container.set_name()Container.set_sample()Container.set_sequence()Container.subset()Container.to_bases()Container.to_codons()Container.upper()
SampleViewSequenceViewLabelViewencodeSitesite_from_align()site_from_list()site_from_vcf()Freqfreq_from_site()freq_from_list()freq_from_vcf()AlphabetStructureStructure.as_dict()Structure.from_dict()Structure.from_iterable()Structure.from_labels()Structure.from_samplesizes()Structure.get_clusters()Structure.get_populations()Structure.get_samples()Structure.make_auxiliary()Structure.make_sorted_auxiliary()Structure.noStructure.nsStructure.num_clustStructure.num_indiv_ingroupStructure.num_indiv_outgroupStructure.num_popStructure.ploidyStructure.req_nsStructure.shuffle()Structure.subset()
struct_from_labels()struct_from_samplesizes()struct_from_iterable()struct_from_dict()TreeTree.add_node()Tree.baseTree.breadth_iter()Tree.clean_branch_lengths()Tree.clean_internal_labels()Tree.collapse()Tree.copy()Tree.depth_iter()Tree.extract()Tree.find_clade()Tree.frequency_nodes()Tree.get_leaf()Tree.iter_leaves()Tree.lateralize()Tree.map_descendants()Tree.midroot()Tree.newick()Tree.num_leavesTree.num_nodesTree.remove_node()Tree.root()Tree.total_length()Tree.unroot()
Node
- Pre-defined alphabets
- Pseudorandom number generator
- Sequence manipulation tools
ReadingFrameReadingFrame.codon_bases()ReadingFrame.codon_index()ReadingFrame.codon_position()ReadingFrame.exon_index()ReadingFrame.iter_codons()ReadingFrame.iter_exon_bounds()ReadingFrame.num_codonsReadingFrame.num_exon_basesReadingFrame.num_exonsReadingFrame.num_needed_basesReadingFrame.num_tot_basesReadingFrame.process()
to_codons()to_bases()concat()ungap()ungap_all()rc()compare()regex()motif_iter()translate()Translatororf_iter()longest_orf()backalign()BackalignErrortrailing_stops()iter_stops()has_stop()
- Import/export utilities
to_ms()from_fasta()from_fasta_string()fasta_iterfrom_genepop()GFF3Gff3FeatureVCFVCF.as_site()VCF.dump_close()VCF.dump_record()VCF.get_allele_type()VCF.get_alleles()VCF.get_alternate()VCF.get_chrom()VCF.get_errors()VCF.get_filter()VCF.get_format()VCF.get_formats()VCF.get_genotypes()VCF.get_id()VCF.get_info()VCF.get_infos()VCF.get_phased()VCF.get_pos()VCF.get_quality()VCF.get_reference()VCF.get_sample()VCF.get_samples()VCF.get_types()VCF.goto()VCF.has_indexVCF.is_single()VCF.is_snp()VCF.iter_sites()VCF.num_samplesVCF.read()
index_vcf()VcfSliderCodonVCFCodingSitefrom_clustal()from_staden()from_genalys()get_fgenesh()GenBankGenBankFeatureGenBankFeature.add_qualifier()GenBankFeature.copy()GenBankFeature.format()GenBankFeature.get_sequence()GenBankFeature.get_start()GenBankFeature.get_stop()GenBankFeature.get_type()GenBankFeature.parse()GenBankFeature.qualifiers()GenBankFeature.rc()GenBankFeature.shift()GenBankFeature.update()
GenBankFeatureLocationGenBankFeatureLocation.add_base_choice()GenBankFeatureLocation.add_base_range()GenBankFeatureLocation.add_between_base()GenBankFeatureLocation.add_single_base()GenBankFeatureLocation.as_order()GenBankFeatureLocation.as_range()GenBankFeatureLocation.copy()GenBankFeatureLocation.format()GenBankFeatureLocation.is_complement()GenBankFeatureLocation.is_range()GenBankFeatureLocation.rc()GenBankFeatureLocation.set_complement()GenBankFeatureLocation.set_forward()GenBankFeatureLocation.shift()
- Alternative VCF parser
VcfParserVcfParser.bed_slider()VcfParser.close()VcfParser.currlineVcfParser.file_formatVcfParser.get_alt()VcfParser.get_filter()VcfParser.get_format()VcfParser.get_genotypes()VcfParser.get_info()VcfParser.get_meta()VcfParser.get_sample()VcfParser.get_variant()VcfParser.goodVcfParser.goto()VcfParser.has_indexVcfParser.load_index()VcfParser.num_altVcfParser.num_filterVcfParser.num_formatVcfParser.num_indexVcfParser.num_infoVcfParser.num_metaVcfParser.num_samplesVcfParser.readline()VcfParser.rewind()VcfParser.slider()VcfParser.unread()
make_vcf_index()VcfStringParserVcfStringParser.file_formatVcfStringParser.get_alt()VcfStringParser.get_filter()VcfStringParser.get_format()VcfStringParser.get_genotypes()VcfStringParser.get_info()VcfStringParser.get_meta()VcfStringParser.get_sample()VcfStringParser.get_variant()VcfStringParser.num_altVcfStringParser.num_filterVcfStringParser.num_formatVcfStringParser.num_infoVcfStringParser.num_metaVcfStringParser.num_samplesVcfStringParser.readline()
VcfVariantVcfVariant.alt_type_defaultVcfVariant.alt_type_referredVcfVariant.alt_type_breakendVcfVariant.AAVcfVariant.ACVcfVariant.AFVcfVariant.ANVcfVariant.GLVcfVariant.GTVcfVariant.GT_phasedVcfVariant.GT_vcfVcfVariant.IDVcfVariant.PLVcfVariant.allelesVcfVariant.alternate_typesVcfVariant.chromosomeVcfVariant.failed_testsVcfVariant.format_fieldsVcfVariant.infoVcfVariant.num_allelesVcfVariant.num_alternateVcfVariant.num_genotypesVcfVariant.num_samplesVcfVariant.ploidyVcfVariant.positionVcfVariant.qualityVcfVariant.samples
VcfSlidingWindowVcfWindowFIRSTLASTBED
- Diversity statistics
ComputeStatsComputeStats.add_stats()ComputeStats.all_stats()ComputeStats.clear_stats()ComputeStats.configure()ComputeStats.list_stats()ComputeStats.process_align()ComputeStats.process_freq()ComputeStats.process_site()ComputeStats.process_sites()ComputeStats.reset()ComputeStats.results()ComputeStats.set_structure()ComputeStats.stats_group()
SFS()EHHEHH.cur_haplotypesEHH.done_EHH()EHH.done_EHHc()EHH.get_EHH()EHH.get_EHHG()EHH.get_EHHS()EHH.get_EHHc()EHH.get_dEHH()EHH.get_dEHHG()EHH.get_dEHHS()EHH.get_dEHH_max()EHH.get_dEHH_mean()EHH.get_dEHHc()EHH.get_iEG()EHH.get_iES()EHH.get_iHH()EHH.get_iHHc()EHH.get_iHS()EHH.get_rEHH()EHH.load_distant()EHH.nsamEHH.nsam_core()EHH.nsam_hap()EHH.num_haplotypesEHH.set_core()
pairwise_LD()matrix_LD()ProbaMisorientedhaplotypes_from_align()haplotypes_from_sites()CodingDiversityCodingDiversity.num_codons_effCodingDiversity.num_codons_stopCodingDiversity.num_codons_totCodingDiversity.num_multiple_allelesCodingDiversity.num_multiple_hitsCodingDiversity.num_pol_NSCodingDiversity.num_pol_SCodingDiversity.num_pol_singleCodingDiversity.num_sites_NSCodingDiversity.num_sites_SCodingDiversity.positions_NSCodingDiversity.positions_SCodingDiversity.process()CodingDiversity.sites_NSCodingDiversity.sites_S
paralog_pi()ParalogPi
- Coalescent simulator
- External application tools
phyml()codeml()nj()clustal()muscle()muscle5()muscle3()makeblastdb()megablast()dc_megablast()blastn()blastn_short()blastp()blastp_short()blastp_fast()blastx()blastx_fast()tblastn()tblastn_fast()tblastx()BlastOutputBlastOutput.dbBlastOutput.get_query()BlastOutput.iter_hits()BlastOutput.iter_hsp()BlastOutput.iter_queries()BlastOutput.num_hitsBlastOutput.num_hspBlastOutput.num_queriesBlastOutput.paramsBlastOutput.programBlastOutput.query_IDBlastOutput.query_defBlastOutput.query_lenBlastOutput.referenceBlastOutput.version
BlastQueryHitsBlastQueryHits.HBlastQueryHits.KBlastQueryHits.LBlastQueryHits.db_lenBlastQueryHits.db_numBlastQueryHits.eff_spaceBlastQueryHits.get_hit()BlastQueryHits.hsp_lenBlastQueryHits.iter_hits()BlastQueryHits.iter_hsp()BlastQueryHits.numBlastQueryHits.num_hitsBlastQueryHits.num_hspBlastQueryHits.query_IDBlastQueryHits.query_defBlastQueryHits.query_len
BlastHitBlastHsp- Configuring paths
- Top level components