Index

A

add_alignment() (pylprotpredictor.cds.CDS method) add_alternative_cds() (pylprotpredictor.cds.CDS method)

add_id_alignment() (pylprotpredictor.cds.CDS method) add_rejected_cds() (pylprotpredictor.cds.CDS method) Alignment (class in pylprotpredictor.alignment)

C

CDS (class in pylprotpredictor.cds)

check_pyl_proteins() (in module pylprotpredictor.check)

E

export_description() (pylprotpredictor.cds.CDS method) export_to_dict() (pylprotpredictor.cds.CDS method) extract_correct_cds() (in module pylprotpredictor.check) extract_possible_alternative_seq() (pylprotpredictor.cds.CDS method)

extract_potential_pyl_cds() (in module pylprotpredictor.predict) extract_predicted_cds() (in module pylprotpredictor.predict) extract_row_number() (in module pylprotpredictor.write_report) extract_seq_desc() (in module pylprotpredictor.cds) extract_seqs() (in module pylprotpredictor.predict)

F

find_alternative_ends() (pylprotpredictor.cds.CDS method)

find_stop_codon_pos_in_seq() (in module pylprotpredictor.cds)

G

get_alignments() (pylprotpredictor.cds.CDS method) get_alternative_cds() (pylprotpredictor.cds.CDS method) get_alternative_end() (pylprotpredictor.cds.CDS method) get_alternative_ends() (pylprotpredictor.cds.CDS method) get_alternative_start() (pylprotpredictor.cds.CDS method) get_bitscore() (pylprotpredictor.alignment.Alignment method) get_cds_obj() (in module pylprotpredictor.check) get_conserved_cds() (pylprotpredictor.cds.CDS method) get_end() (pylprotpredictor.cds.CDS method) get_evalue() (pylprotpredictor.alignment.Alignment method) get_gapopen() (pylprotpredictor.alignment.Alignment method) get_highest_bitscore() (pylprotpredictor.cds.CDS method) get_id() (pylprotpredictor.cds.CDS method) get_length() (pylprotpredictor.alignment.Alignment method) get_lowest_evalue_alignment() (pylprotpredictor.cds.CDS method) get_mismatch() (pylprotpredictor.alignment.Alignment method) get_origin_seq() (pylprotpredictor.cds.CDS method)

get_origin_seq_id() (pylprotpredictor.cds.CDS method) get_origin_seq_size() (pylprotpredictor.cds.CDS method) get_origin_seq_string() (pylprotpredictor.cds.CDS method) get_pident() (pylprotpredictor.alignment.Alignment method) get_qend() (pylprotpredictor.alignment.Alignment method) get_qstart() (pylprotpredictor.alignment.Alignment method) get_rejected_cds() (pylprotpredictor.cds.CDS method) get_send() (pylprotpredictor.alignment.Alignment method) get_seq() (pylprotpredictor.cds.CDS method) get_seqrecord() (pylprotpredictor.cds.CDS method) get_sseqid() (pylprotpredictor.alignment.Alignment method) get_sstart() (pylprotpredictor.alignment.Alignment method) get_start() (pylprotpredictor.cds.CDS method) get_status() (pylprotpredictor.cds.CDS method) get_stop_codon() (pylprotpredictor.cds.CDS method) get_strand() (pylprotpredictor.cds.CDS method) get_translated_alternative_seq() (pylprotpredictor.cds.CDS method) get_translated_seq() (pylprotpredictor.cds.CDS method)

H

has_alternative_cds() (pylprotpredictor.cds.CDS method)

has_alternative_ends() (pylprotpredictor.cds.CDS method) has_origin_seq() (pylprotpredictor.cds.CDS method)

I

identify_cons_rej_cds() (pylprotpredictor.cds.CDS method) import_cds() (in module pylprotpredictor.check) init_from_dict() (pylprotpredictor.cds.CDS method) init_from_record() (pylprotpredictor.cds.CDS method)

init_from_search_report_row() (pylprotpredictor.alignment.Alignment method) is_potential_pyl() (pylprotpredictor.cds.CDS method) is_reverse_strand() (pylprotpredictor.cds.CDS method) is_tag_ending() (pylprotpredictor.cds.CDS method) is_tag_ending_seq() (pylprotpredictor.cds.CDS method)

P

parse_similarity_search_report() (in module pylprotpredictor.check) predict_pyl_proteins() (in module pylprotpredictor.predict) pylprotpredictor.alignment (module)

pylprotpredictor.cds (module) pylprotpredictor.check (module) pylprotpredictor.predict (module) pylprotpredictor.write_report (module)

R

reset_alignments() (pylprotpredictor.cds.CDS method)

reset_alternative_cds() (pylprotpredictor.cds.CDS method) reset_rejected_cds() (pylprotpredictor.cds.CDS method)

S

set_alternative_ends() (pylprotpredictor.cds.CDS method) set_bitscore() (pylprotpredictor.alignment.Alignment method) set_conserved_cds() (pylprotpredictor.cds.CDS method) set_end() (pylprotpredictor.cds.CDS method) set_evalue() (pylprotpredictor.alignment.Alignment method) (pylprotpredictor.cds.CDS method) set_gapopen() (pylprotpredictor.alignment.Alignment method) set_id() (pylprotpredictor.cds.CDS method) set_length() (pylprotpredictor.alignment.Alignment method) set_mismatch() (pylprotpredictor.alignment.Alignment method) set_origin_seq() (pylprotpredictor.cds.CDS method)

set_origin_seq_id() (pylprotpredictor.cds.CDS method) set_pident() (pylprotpredictor.alignment.Alignment method) set_qend() (pylprotpredictor.alignment.Alignment method) set_qstart() (pylprotpredictor.alignment.Alignment method) set_send() (pylprotpredictor.alignment.Alignment method) set_seq() (pylprotpredictor.cds.CDS method) set_sseqid() (pylprotpredictor.alignment.Alignment method) set_sstart() (pylprotpredictor.alignment.Alignment method) set_start() (pylprotpredictor.cds.CDS method) set_status() (pylprotpredictor.cds.CDS method) set_strand() (pylprotpredictor.cds.CDS method)

T

test_to_continue() (in module pylprotpredictor.cds)

transform_strand() (in module pylprotpredictor.cds) translate() (in module pylprotpredictor.cds)

W

write_report() (in module pylprotpredictor.write_report)