Index

_

__str__() (CodonU.cua_errors.codon_usage_err.CodonUsageError method) _enc() (in module CodonU.vizualizer.plot_funcs) _plot_enc() (in module CodonU.vizualizer.plot_funcs)

_plot_neutrality() (in module CodonU.vizualizer.plot_funcs) _plot_pr2() (in module CodonU.vizualizer.plot_funcs) _print_msg() (in module CodonU.analyzer.generate_report) (in module CodonU.analyzer.generate_report_summary)

A

a3() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) ApiWarning (class in CodonU.cua_warnings) (class in CodonU.cua_warnings.api_warn)

aromaticity() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) at_123() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

B

BadSequenceError, [1], [2] build_contingency_table_aa_count() (in module CodonU.correspondence_analysis) (in module CodonU.correspondence_analysis.build_contingency_table_aa_count)

build_contingency_table_codon_count() (in module CodonU.correspondence_analysis) (in module CodonU.correspondence_analysis.build_contingency_table_codon_count) build_contingency_table_codon_rscu() (in module CodonU.correspondence_analysis) (in module CodonU.correspondence_analysis.build_contingency_table_codon_rscu)

C

ca_aa() (in module CodonU.correspondence_analysis) (in module CodonU.correspondence_analysis.ca_aa) ca_codon() (in module CodonU.correspondence_analysis) (in module CodonU.correspondence_analysis.ca_codon) CAComponentWarn (class in CodonU.cua_warnings) (class in CodonU.cua_warnings.ca_component_warn) cai() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) calculate_aromaticity() (in module CodonU.analyzer) (in module CodonU.analyzer.aromaticity_comp) calculate_cai() (in module CodonU.analyzer) (in module CodonU.analyzer.cai_comp) calculate_cbi() (in module CodonU.analyzer) (in module CodonU.analyzer.cbi_comp) calculate_enc() (in module CodonU.analyzer) (in module CodonU.analyzer.enc_comp) calculate_gravy() (in module CodonU.analyzer) (in module CodonU.analyzer.gravy_comp) calculate_gtai() (in module CodonU.analyzer) (in module CodonU.analyzer.tRNA_comp) calculate_rscu() (in module CodonU.analyzer) (in module CodonU.analyzer.rscu_comp) cbi() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) CodonTableExistsError, [1], [2] CodonU module CodonU.analyzer module CodonU.analyzer.aromaticity_comp module CodonU.analyzer.cai_comp module CodonU.analyzer.cbi_comp module CodonU.analyzer.enc_comp module CodonU.analyzer.generate_report module CodonU.analyzer.generate_report_summary module CodonU.analyzer.gravy_comp module CodonU.analyzer.internal_comp module CodonU.analyzer.rscu_comp module CodonU.analyzer.tRNA_comp module CodonU.correspondence_analysis module CodonU.correspondence_analysis.build_contingency_table_aa_count module CodonU.correspondence_analysis.build_contingency_table_codon_count module CodonU.correspondence_analysis.build_contingency_table_codon_rscu module CodonU.correspondence_analysis.ca_aa module CodonU.correspondence_analysis.ca_codon module CodonU.cua_errors module CodonU.cua_errors.bad_seq_err module CodonU.cua_errors.codon_table_exist_err module CodonU.cua_errors.codon_usage_err module CodonU.cua_errors.file_not_empty_err module CodonU.cua_errors.internal_stop_codon_err module CodonU.cua_errors.no_prot_err module CodonU.cua_errors.nucleotide_err module CodonU.cua_errors.ter_seq_err module CodonU.cua_errors.unsupported_db module CodonU.cua_errors.unsupported_type module CodonU.cua_warnings module

CodonU.cua_warnings.api_warn module CodonU.cua_warnings.ca_component_warn module CodonU.cua_warnings.codon_usage_warns module CodonU.cua_warnings.email_warn module CodonU.cua_warnings.missing_codon_warn module CodonU.cua_warnings.no_codon_warn module CodonU.cua_warnings.no_syn_codon_warn module CodonU.extractor module CodonU.extractor.extract_cds module CodonU.extractor.extract_cds_lst module CodonU.extractor.extract_exome module CodonU.extractor.extract_prot module CodonU.extractor.internal_comp module CodonU.file_handler module CodonU.file_handler.get_gb module CodonU.file_handler.internal_comp module CodonU.file_handler.make_dir module CodonU.file_handler.read_file module CodonU.file_handler.set_entrez_param module CodonU.file_handler.write_exome_fasta module CodonU.file_handler.write_nucleotide_fasta module CodonU.file_handler.write_protein_fasta module CodonU.phylogenetic_analysis module CodonU.phylogenetic_analysis.clustal_o module CodonU.phylogenetic_analysis.clustal_w module CodonU.phylogenetic_analysis.generate_phylo_input module CodonU.vizualizer module CodonU.vizualizer.plot_ca_aa_freq_aa module CodonU.vizualizer.plot_ca_aa_freq_gene module CodonU.vizualizer.plot_ca_codon_freq_codon module CodonU.vizualizer.plot_ca_codon_freq_gene module CodonU.vizualizer.plot_ca_codon_rscu_codon module CodonU.vizualizer.plot_ca_codon_rscu_gene module CodonU.vizualizer.plot_enc module CodonU.vizualizer.plot_funcs module CodonU.vizualizer.plot_neutrality module CodonU.vizualizer.plot_phy_dnd module CodonU.vizualizer.plot_phy_fas module CodonU.vizualizer.plot_phy_nex module CodonU.vizualizer.plot_pr2 module CodonUsageError CodonUsageWarning custom_codon_table() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

E

EmailWarning, [1] enc() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) extract_cds() (in module CodonU.extractor) (in module CodonU.extractor.extract_cds) extract_cds_lst() (in module CodonU.extractor) (in module CodonU.extractor.extract_cds_lst)

extract_cds_seq() (in module CodonU.extractor.internal_comp) extract_exome() (in module CodonU.extractor) (in module CodonU.extractor.extract_exome) extract_prot() (in module CodonU.extractor) (in module CodonU.extractor.extract_prot) extract_prot_seq() (in module CodonU.extractor.internal_comp)

F

FileNotEmptyError, [1]

filter_reference() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

G

g3() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) gc_123() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) generate_phylo_input() (in module CodonU.phylogenetic_analysis) (in module CodonU.phylogenetic_analysis.generate_phylo_input) generate_report() (in module CodonU.analyzer) (in module CodonU.analyzer.generate_report)

generate_report_summary() (in module CodonU.analyzer.generate_report_summary) get_anticodon_count_dict() (in module CodonU.analyzer) (in module CodonU.analyzer.tRNA_comp) get_gb() (in module CodonU.file_handler) (in module CodonU.file_handler.get_gb) gravy() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

I

InternalStopCodonError, [1] is_file() (in module CodonU.file_handler.internal_comp) is_file_empty() (in module CodonU.file_handler.internal_comp)

is_file_writeable() (in module CodonU.file_handler.internal_comp) is_not_bad_seq() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

M

make_dir() (in module CodonU.file_handler) (in module CodonU.file_handler.make_dir) MissingCodonWarning, [1], [2] module CodonU CodonU.analyzer CodonU.analyzer.aromaticity_comp CodonU.analyzer.cai_comp CodonU.analyzer.cbi_comp CodonU.analyzer.enc_comp CodonU.analyzer.generate_report CodonU.analyzer.generate_report_summary CodonU.analyzer.gravy_comp CodonU.analyzer.internal_comp CodonU.analyzer.rscu_comp CodonU.analyzer.tRNA_comp CodonU.correspondence_analysis CodonU.correspondence_analysis.build_contingency_table_aa_count CodonU.correspondence_analysis.build_contingency_table_codon_count CodonU.correspondence_analysis.build_contingency_table_codon_rscu CodonU.correspondence_analysis.ca_aa CodonU.correspondence_analysis.ca_codon CodonU.cua_errors CodonU.cua_errors.bad_seq_err CodonU.cua_errors.codon_table_exist_err CodonU.cua_errors.codon_usage_err CodonU.cua_errors.file_not_empty_err CodonU.cua_errors.internal_stop_codon_err CodonU.cua_errors.no_prot_err CodonU.cua_errors.nucleotide_err CodonU.cua_errors.ter_seq_err CodonU.cua_errors.unsupported_db CodonU.cua_errors.unsupported_type CodonU.cua_warnings CodonU.cua_warnings.api_warn CodonU.cua_warnings.ca_component_warn CodonU.cua_warnings.codon_usage_warns CodonU.cua_warnings.email_warn CodonU.cua_warnings.missing_codon_warn CodonU.cua_warnings.no_codon_warn CodonU.cua_warnings.no_syn_codon_warn CodonU.extractor CodonU.extractor.extract_cds CodonU.extractor.extract_cds_lst CodonU.extractor.extract_exome CodonU.extractor.extract_prot CodonU.extractor.internal_comp CodonU.file_handler CodonU.file_handler.get_gb CodonU.file_handler.internal_comp CodonU.file_handler.make_dir CodonU.file_handler.read_file CodonU.file_handler.set_entrez_param CodonU.file_handler.write_exome_fasta CodonU.file_handler.write_nucleotide_fasta CodonU.file_handler.write_protein_fasta CodonU.phylogenetic_analysis CodonU.phylogenetic_analysis.clustal_o CodonU.phylogenetic_analysis.clustal_w CodonU.phylogenetic_analysis.generate_phylo_input CodonU.vizualizer CodonU.vizualizer.plot_ca_aa_freq_aa CodonU.vizualizer.plot_ca_aa_freq_gene CodonU.vizualizer.plot_ca_codon_freq_codon CodonU.vizualizer.plot_ca_codon_freq_gene CodonU.vizualizer.plot_ca_codon_rscu_codon CodonU.vizualizer.plot_ca_codon_rscu_gene CodonU.vizualizer.plot_enc CodonU.vizualizer.plot_funcs CodonU.vizualizer.plot_neutrality CodonU.vizualizer.plot_phy_dnd CodonU.vizualizer.plot_phy_fas CodonU.vizualizer.plot_phy_nex CodonU.vizualizer.plot_pr2

N

NoCodonWarning (class in CodonU.cua_warnings) (class in CodonU.cua_warnings.no_codon_warn) NoProteinError, [1], [2]

NoSynonymousCodonWarning, [1], [2] not_contains_amb_letter() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) NucleotideError, [1], [2]

P

phy_clustal_o() (in module CodonU.phylogenetic_analysis) (in module CodonU.phylogenetic_analysis.clustal_o) phy_clustal_w() (in module CodonU.phylogenetic_analysis) (in module CodonU.phylogenetic_analysis.clustal_w) plot_ca_aa_freq_aa() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_aa_freq_aa) plot_ca_aa_freq_gene() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_aa_freq_gene) plot_ca_codon_freq_codon() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_codon_freq_codon) plot_ca_codon_freq_gene() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_codon_freq_gene) plot_ca_codon_rscu_codon() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_codon_rscu_codon)

plot_ca_codon_rscu_gene() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_ca_codon_rscu_gene) plot_enc() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_enc) plot_neutrality() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_neutrality) plot_phy_dnd() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_phy_dnd) plot_phy_fas() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_phy_fas) plot_phy_nex() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_phy_nex) plot_pr2() (in module CodonU.vizualizer) (in module CodonU.vizualizer.plot_pr2)

R

read_file() (in module CodonU.file_handler) (in module CodonU.file_handler.read_file) reverse_table() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

rscu() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

S

set_entrez_api_key() (in module CodonU.file_handler.internal_comp) set_entrez_email() (in module CodonU.file_handler.internal_comp) set_entrez_param() (in module CodonU.file_handler) (in module CodonU.file_handler.set_entrez_param)

sf_vals() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) syn_codons() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp)

T

TerSeqError, [1]

U

UnsupportedDatabase, [1]

UnsupportedType, [1]

W

warn() (CodonU.analyzer.MissingCodonWarning method) (CodonU.analyzer.NoSynonymousCodonWarning method) (CodonU.cua_warnings.api_warn.ApiWarning method) (CodonU.cua_warnings.ApiWarning method) (CodonU.cua_warnings.ca_component_warn.CAComponentWarn method) (CodonU.cua_warnings.CAComponentWarn method) (CodonU.cua_warnings.email_warn.EmailWarning method) (CodonU.cua_warnings.EmailWarning method) (CodonU.cua_warnings.missing_codon_warn.MissingCodonWarning method) (CodonU.cua_warnings.MissingCodonWarning method) (CodonU.cua_warnings.no_codon_warn.NoCodonWarning method) (CodonU.cua_warnings.no_syn_codon_warn.NoSynonymousCodonWarning method) (CodonU.cua_warnings.NoCodonWarning method) (CodonU.cua_warnings.NoSynonymousCodonWarning method)

weights_for_cai() (in module CodonU.analyzer) (in module CodonU.analyzer.internal_comp) write_exome_fasta() (in module CodonU.file_handler) (in module CodonU.file_handler.write_exome_fasta) write_nucleotide_fasta() (in module CodonU.file_handler) (in module CodonU.file_handler.write_nucleotide_fasta) write_protein_fasta() (in module CodonU.file_handler) (in module CodonU.file_handler.write_protein_fasta)