Index

A | B | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W

A

a() (in module libPoMo.main)
add_base_to_sequence() (libPoMo.cf.CFWriter method)
append_nuc_base() (libPoMo.vcf.VCFSeq method)

B

binom() (in module libPoMo.main)

C

cf_to_fasta() (in module libPoMo.cf)
CFStream (class in libPoMo.cf)
CFWriter (class in libPoMo.cf)
check_fixed_field_header() (in module libPoMo.vcf)
close() (libPoMo.cf.CFWriter method)
(libPoMo.fasta.FaStream method)
(libPoMo.fasta.MFaStream method)
(libPoMo.vcf.VCFStream method)
CountsFormatWriterError

D

dsRatio() (in module libPoMo.main)

F

FaSeq (class in libPoMo.fasta)
faseq_append_base_of_cfS() (in module libPoMo.cf)
fasta_to_cf() (in module libPoMo.cf)
FaStream (class in libPoMo.fasta)
filter_mfa_str() (in module libPoMo.fasta)

G

get_alt_base_list() (libPoMo.vcf.NucBase method)
get_base() (libPoMo.seqbase.Seq method)
get_base_ind() (libPoMo.vcf.NucBase method)
get_data_from_cf_line() (in module libPoMo.main)
get_distance() (libPoMo.fasta.FaSeq method)
get_exon_nr() (libPoMo.seqbase.Seq method)
get_header_line_string() (in module libPoMo.vcf)
(libPoMo.vcf.VCFSeq method)
get_in_frame() (libPoMo.seqbase.Seq method)
get_indiv_from_field_header() (in module libPoMo.vcf)
get_info() (libPoMo.vcf.NucBase method)
get_nuc_base() (libPoMo.vcf.VCFSeq method)
get_nuc_base_from_line() (in module libPoMo.vcf)
get_out_frame() (libPoMo.seqbase.Seq method)
get_rc() (libPoMo.seqbase.Seq method)
get_ref_base() (libPoMo.vcf.NucBase method)
get_region() (libPoMo.seqbase.Seq method)
get_region_no_description() (libPoMo.seqbase.Seq method)
get_seq_base() (libPoMo.fasta.FaSeq method)
get_seq_by_id() (libPoMo.fasta.FaSeq method)
get_seq_names() (libPoMo.fasta.FaSeq method)
get_species_from_cf_headerline() (in module libPoMo.main)
get_speciesData() (libPoMo.vcf.NucBase method)
gz_open() (in module libPoMo.seqbase)

H

has_base() (libPoMo.vcf.VCFSeq method)

I

init_seq() (in module libPoMo.fasta)
(in module libPoMo.vcf)
interpret_cf_line() (in module libPoMo.cf)
is_number() (in module libPoMo.main)
is_synonymous() (libPoMo.seqbase.Seq method)

L

libPoMo.cf (module)
libPoMo.fasta (module)
libPoMo.main (module)
libPoMo.seqbase (module)
libPoMo.vcf (module)

M

MFaStream (class in libPoMo.fasta)
MFaStrFilterProps (class in libPoMo.fasta)
mutModel() (in module libPoMo.main)

N

NoSynBase
NotACountsFormatFileError
NotAFastaFileError
NotANucBaseError
NotAValidRefBase
NotAVariantCallFormatFileError
NucBase (class in libPoMo.vcf)

O

open_seq() (in module libPoMo.fasta)
(in module libPoMo.vcf)
orient() (libPoMo.fasta.MFaStream method)

P

print_data() (libPoMo.seqbase.Seq method)
print_fa_entry() (libPoMo.seqbase.Seq method)
print_fa_header() (libPoMo.seqbase.Seq method)
print_header_line() (libPoMo.vcf.VCFSeq method)
print_info() (libPoMo.fasta.FaSeq method)
(libPoMo.fasta.FaStream method)
(libPoMo.fasta.MFaStream method)
(libPoMo.seqbase.Region method)
(libPoMo.seqbase.Seq method)
(libPoMo.vcf.NucBase method)
(libPoMo.vcf.VCFSeq method)
(libPoMo.vcf.VCFStream method)
print_msa() (libPoMo.fasta.MFaStream method)
probability_matrix() (in module libPoMo.main)
purge() (libPoMo.seqbase.Seq method)
(libPoMo.vcf.NucBase method)

R

read_align_from_fo() (in module libPoMo.fasta)
read_data_write_HyPhy_input() (in module libPoMo.main)
read_next_align() (libPoMo.fasta.MFaStream method)
read_next_base() (libPoMo.vcf.VCFStream method)
read_next_pos() (libPoMo.cf.CFStream method)
read_next_seq() (libPoMo.fasta.FaStream method)
read_seq_from_fo() (in module libPoMo.fasta)
Region (class in libPoMo.seqbase)
rev_comp() (libPoMo.seqbase.Seq method)

S

save_as_vcf() (in module libPoMo.fasta)
selModel() (in module libPoMo.main)
Seq (class in libPoMo.seqbase)
SequenceDataError
set_force() (libPoMo.cf.CFWriter method)
set_offset() (libPoMo.cf.CFWriter method)
set_ploidy() (libPoMo.cf.CFWriter method)
(libPoMo.vcf.NucBase method)
set_rc() (libPoMo.seqbase.Seq method)
set_seq() (libPoMo.cf.CFWriter method)
setGM() (in module libPoMo.main)
setGS() (in module libPoMo.main)
stripFName() (in module libPoMo.seqbase)

T

timeStr() (in module libPoMo.main)
toggle_rc() (libPoMo.seqbase.Seq method)

U

update_base() (in module libPoMo.vcf)

V

VCFSeq (class in libPoMo.vcf)
VCFStream (class in libPoMo.vcf)

W

weighted_choice() (in module libPoMo.cf)
write_cf_from_gp_stream() (in module libPoMo.cf)
write_cf_from_MFaStream() (in module libPoMo.cf)
write_HLn() (libPoMo.cf.CFWriter method)
write_Ln() (libPoMo.cf.CFWriter method)
write_Rn() (libPoMo.cf.CFWriter method)