dinopy
latest
Getting Started
Note about dtype
dinopy
Changelog
FAQ
dinopy
Index
Edit on Bitbucket
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
_
__getitem__() (dinopy.definitions.FastaChromosomeC method)
(dinopy.definitions.FastaChromosomeInfoC method)
(dinopy.definitions.FastaEntryC method)
(dinopy.definitions.FastaGenomeC method)
(dinopy.definitions.FastaReadC method)
(dinopy.definitions.FastqLineC method)
(dinopy.definitions.FastqReadC method)
(dinopy.definitions.FastqReadWithoutNameC method)
(dinopy.definitions.FastqReadWithoutQVC method)
(dinopy.definitions.IUPACRandomReplacementDict method)
A
AlignmentRecord (class in dinopy.sambam)
apply_shape() (in module dinopy.shaping)
B
basenumbers (class in dinopy.definitions)
basenumbers_to_bytes() (in module dinopy.conversion)
basenumbers_to_string() (in module dinopy.conversion)
bit_base (class in dinopy.definitions)
bool_shape (dinopy.shape.Shape attribute)
bytes_to_basenumbers() (in module dinopy.conversion)
bytes_to_string() (in module dinopy.conversion)
C
chromosome_info_to_fai() (in module dinopy.fai_io)
ChromosomeFormatError
chromosomes() (dinopy.fasta_reader.FastaReader method)
cigar (dinopy.sambam.AlignmentRecord attribute)
cigar_str_from_pysam_cigartuples() (in module dinopy.sambam)
cigar_str_from_tuples() (in module dinopy.sambam)
close() (dinopy.creader.CReader method)
(dinopy.fasta_writer.FastaWriter method)
(dinopy.sam_writer.SamWriter method)
closed (dinopy.creader.CReader attribute)
complement() (in module dinopy.processors)
complement_2bit() (in module dinopy.processors)
complement_4bit() (in module dinopy.processors)
CReader (class in dinopy.creader)
create_flag() (in module dinopy.sambam)
create_header_sq_lines() (dinopy.sam_writer.SamWriter method)
D
decode() (in module dinopy.conversion)
decode_fourbit() (in module dinopy.conversion)
decode_twobit() (in module dinopy.conversion)
dinopy.auxiliary
module
dinopy.conversion
module
dinopy.creader
module
dinopy.definitions
module
dinopy.exceptions
module
dinopy.fai_io
module
dinopy.fasta_reader
module
dinopy.fasta_writer
module
dinopy.fastq_reader
module
dinopy.fastq_writer
module
dinopy.input_opener
module
dinopy.nameline_parser
module
dinopy.processors
module
dinopy.sam_reader
module
dinopy.sam_writer
module
dinopy.sambam
module
dinopy.shaping
module
E
encode() (in module dinopy.conversion)
encode_fourbit() (in module dinopy.conversion)
encode_twobit() (in module dinopy.conversion)
entries() (dinopy.fasta_reader.FastaReader method)
F
fai_entry_to_chromosome_info_entry() (in module dinopy.fai_io)
fai_to_chromosome_info() (in module dinopy.fai_io)
FastaChromosomeC (class in dinopy.definitions)
FastaChromosomeInfoC (class in dinopy.definitions)
FastaEntryC (class in dinopy.definitions)
FastaGenomeC (class in dinopy.definitions)
FastaReadC (class in dinopy.definitions)
FastaReader (class in dinopy.fasta_reader)
FastaWriter (class in dinopy.fasta_writer)
FastqLineC (class in dinopy.definitions)
FastqReadC (class in dinopy.definitions)
FastqReader (class in dinopy.fastq_reader)
FastqReadWithoutNameC (class in dinopy.definitions)
FastqReadWithoutQVC (class in dinopy.definitions)
FastqWriter (class in dinopy.fastq_writer)
fileno() (dinopy.creader.CReader method)
flag (dinopy.sambam.AlignmentRecord attribute)
flush() (dinopy.creader.CReader method)
four_bit (class in dinopy.definitions)
fromdict() (dinopy.sambam.AlignmentRecord class method)
fromkeywords() (dinopy.sambam.AlignmentRecord class method)
fromstr() (dinopy.sambam.AlignmentRecord class method)
fromvalues() (dinopy.sambam.AlignmentRecord class method)
G
genome() (dinopy.fasta_reader.FastaReader method)
get_flag_description() (in module dinopy.sambam)
get_header() (dinopy.sam_reader.SamReader method)
get_inverse_codemap_from_twobit() (in module dinopy.conversion)
get_sam_repr() (dinopy.sambam.AlignmentRecord method)
guess_quality_format() (dinopy.fastq_reader.FastqReader method)
I
illumina13_to_phred() (in module dinopy.conversion)
illumina15_to_phred() (in module dinopy.conversion)
illumina18_to_phred() (in module dinopy.conversion)
index_shape_care (dinopy.shape.Shape attribute)
index_shape_dont_care (dinopy.shape.Shape attribute)
info (dinopy.definitions.FastaGenomeC attribute)
InputOpener (class in dinopy.input_opener)
interval (dinopy.definitions.FastaChromosomeInfoC attribute)
(dinopy.definitions.FastaEntryC attribute)
InvalidDtypeError
InvalidEncodingError
InvalidIUPACAmbiguityCodeError
InvalidLinetypeError
InvalidStartingCharacterError
is_solid() (dinopy.shape.Shape method)
is_valid_fai() (in module dinopy.fai_io)
is_valid_fai_entry() (in module dinopy.fai_io)
isatty() (dinopy.creader.CReader method)
IUPACRandomReplacementDict (class in dinopy.definitions)
L
length (dinopy.definitions.FastaChromosomeC attribute)
(dinopy.definitions.FastaChromosomeInfoC attribute)
(dinopy.definitions.FastaEntryC attribute)
(dinopy.shape.Shape attribute)
lines() (dinopy.fasta_reader.FastaReader method)
(dinopy.fastq_reader.FastqReader method)
M
MalformedFASTAError
mapping_quality (dinopy.sambam.AlignmentRecord attribute)
module
dinopy.auxiliary
dinopy.conversion
dinopy.creader
dinopy.definitions
dinopy.exceptions
dinopy.fai_io
dinopy.fasta_reader
dinopy.fasta_writer
dinopy.fastq_reader
dinopy.fastq_writer
dinopy.input_opener
dinopy.nameline_parser
dinopy.processors
dinopy.sam_reader
dinopy.sam_writer
dinopy.sambam
dinopy.shaping
N
name (dinopy.definitions.FastaChromosomeC attribute)
(dinopy.definitions.FastaChromosomeInfoC attribute)
(dinopy.definitions.FastaEntryC attribute)
(dinopy.definitions.FastaReadC attribute)
(dinopy.definitions.FastqReadC attribute)
(dinopy.definitions.FastqReadWithoutQVC attribute)
NamelineParser (class in dinopy.nameline_parser)
num_care (dinopy.shape.Shape attribute)
num_dont_care (dinopy.shape.Shape attribute)
O
open() (dinopy.creader.CReader method)
optional (dinopy.sambam.AlignmentRecord attribute)
optional_raw (dinopy.sambam.AlignmentRecord attribute)
P
parse() (dinopy.nameline_parser.NamelineParser method)
parse_casava_18_line() (in module dinopy.nameline_parser)
parse_casava_pre18_line() (in module dinopy.nameline_parser)
parse_ncbi_line() (in module dinopy.nameline_parser)
phred_to_illumina13() (in module dinopy.conversion)
phred_to_illumina15() (in module dinopy.conversion)
phred_to_illumina18() (in module dinopy.conversion)
phred_to_sanger() (in module dinopy.conversion)
phred_to_solexa() (in module dinopy.conversion)
pnext (dinopy.sambam.AlignmentRecord attribute)
pos (dinopy.sambam.AlignmentRecord attribute)
print_quality_tally() (dinopy.fastq_reader.FastqReader method)
pysam_cigartuples_from_cigar_str() (in module dinopy.sambam)
Q
qgram_generator() (in module dinopy.auxiliary)
qgrams() (in module dinopy.processors)
qual (dinopy.sambam.AlignmentRecord attribute)
quality (dinopy.definitions.FastqReadC attribute)
(dinopy.definitions.FastqReadWithoutNameC attribute)
quality_tally (dinopy.fastq_reader.FastqReader attribute)
query_name (dinopy.sambam.AlignmentRecord attribute)
query_sequence (dinopy.sambam.AlignmentRecord attribute)
R
random_access() (dinopy.fasta_reader.FastaReader method)
read() (dinopy.creader.CReader method)
read_fai() (in module dinopy.fai_io)
readable() (dinopy.creader.CReader method)
readinto() (dinopy.creader.CReader method)
readline() (dinopy.creader.CReader method)
readlines() (dinopy.creader.CReader method)
reads() (dinopy.fasta_reader.FastaReader method)
(dinopy.fastq_reader.FastqReader method)
records() (dinopy.sam_reader.SamReader method)
replace_ambiguities() (in module dinopy.processors)
reverse_complement() (in module dinopy.processors)
reverse_complement_2bit() (in module dinopy.processors)
reverse_complement_4bit() (in module dinopy.processors)
rname (dinopy.sambam.AlignmentRecord attribute)
rnext (dinopy.sambam.AlignmentRecord attribute)
S
SamReader (class in dinopy.sam_reader)
SamWriter (class in dinopy.sam_writer)
sanger_to_phred() (in module dinopy.conversion)
seek() (dinopy.creader.CReader method)
seekable() (dinopy.creader.CReader method)
sequence (dinopy.definitions.FastaChromosomeC attribute)
(dinopy.definitions.FastaEntryC attribute)
(dinopy.definitions.FastaGenomeC attribute)
(dinopy.definitions.FastaReadC attribute)
(dinopy.definitions.FastqReadC attribute)
(dinopy.definitions.FastqReadWithoutNameC attribute)
(dinopy.definitions.FastqReadWithoutQVC attribute)
Shape (class in dinopy.shape)
solexa_to_phred() (in module dinopy.conversion)
string_list_to_basenumbers() (in module dinopy.conversion)
string_sublists_to_basenumbers() (in module dinopy.conversion)
string_to_basenumbers() (in module dinopy.conversion)
string_to_bytes() (in module dinopy.conversion)
suffix_array() (in module dinopy.processors)
T
tell() (dinopy.creader.CReader method)
template_length (dinopy.sambam.AlignmentRecord attribute)
TooManyCharactersError
truncate() (dinopy.creader.CReader method)
tuples_from_cigar_str() (in module dinopy.sambam)
two_bit (class in dinopy.definitions)
type (dinopy.definitions.FastqLineC attribute)
U
UnknownCharactersError
V
value (dinopy.definitions.FastqLineC attribute)
W
windows() (in module dinopy.shaping)
windows_list() (in module dinopy.shaping)
writable() (dinopy.creader.CReader method)
write() (dinopy.fastq_writer.FastqWriter method)
write_chromosome() (dinopy.fasta_writer.FastaWriter method)
write_chromosomes() (dinopy.fasta_writer.FastaWriter method)
write_chromosomes_as_fai() (in module dinopy.fai_io)
write_entries() (dinopy.fasta_writer.FastaWriter method)
write_entry() (dinopy.fasta_writer.FastaWriter method)
write_fai() (in module dinopy.fai_io)
write_genome() (dinopy.fasta_writer.FastaWriter method)
write_header() (dinopy.sam_writer.SamWriter method)
write_header_line() (dinopy.sam_writer.SamWriter method)
write_reads() (dinopy.fastq_writer.FastqWriter method)
write_record() (dinopy.sam_writer.SamWriter method)
write_records() (dinopy.sam_writer.SamWriter method)
write_sq_header() (dinopy.sam_writer.SamWriter method)
writelines() (dinopy.creader.CReader method)
Read the Docs
v: latest
Versions
latest
stable
Downloads
On Read the Docs
Project Home
Builds