pyhmmer
0.3.0
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Installation
Examples
API Reference
Contributing
Changelog
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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W
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Z
_
__init__() (pyhmmer.easel.Bitfield method)
(pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.SequenceFile method)
(pyhmmer.easel.SSIReader method)
(pyhmmer.easel.SSIWriter method)
(pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.Builder method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.HMMFile method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Pipeline method)
(pyhmmer.plan7.Profile method)
(pyhmmer.plan7.TopHits method)
A
accession (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence attribute)
(pyhmmer.plan7.Hit attribute)
(pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.Profile attribute)
add() (pyhmmer.easel.KeyHash method)
add_alias() (pyhmmer.easel.SSIWriter method)
add_file() (pyhmmer.easel.SSIWriter method)
add_key() (pyhmmer.easel.SSIWriter method)
Alignment (class in pyhmmer.plan7)
AllocationError
Alphabet (class in pyhmmer.easel)
alphabet (pyhmmer.easel.DigitalMSA attribute)
(pyhmmer.easel.DigitalSequence attribute)
amino() (pyhmmer.easel.Alphabet method)
author (pyhmmer.easel.MSA attribute)
B
Background (class in pyhmmer.plan7)
Bitfield (class in pyhmmer.easel)
build() (pyhmmer.plan7.Builder method)
build_msa() (pyhmmer.plan7.Builder method)
Builder (class in pyhmmer.plan7)
C
c_evalue (pyhmmer.plan7.Domain attribute)
checksum (pyhmmer.plan7.HMM attribute)
checksum() (pyhmmer.easel.MSA method)
(pyhmmer.easel.Sequence method)
clear() (pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Sequence method)
(pyhmmer.plan7.Pipeline method)
(pyhmmer.plan7.Profile method)
(pyhmmer.plan7.TopHits method)
close() (pyhmmer.easel.SequenceFile method)
(pyhmmer.easel.SSIReader method)
(pyhmmer.easel.SSIWriter method)
(pyhmmer.plan7.HMMFile method)
configure() (pyhmmer.plan7.Profile method)
consensus (pyhmmer.plan7.HMM attribute)
copy() (pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.KeyHash method)
(pyhmmer.easel.Sequence method)
(pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
(pyhmmer.plan7.Background method)
(pyhmmer.plan7.Builder method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Profile method)
count() (pyhmmer.easel.Bitfield method)
D
data_offset() (pyhmmer.easel.SSIReader.Entry property)
description (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence attribute)
(pyhmmer.plan7.Hit attribute)
(pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.Profile attribute)
DigitalMSA (class in pyhmmer.easel)
DigitalSequence (class in pyhmmer.easel)
digitize() (pyhmmer.easel.TextMSA method)
(pyhmmer.easel.TextSequence method)
dna() (pyhmmer.easel.Alphabet method)
Domain (class in pyhmmer.plan7)
Domains (class in pyhmmer.plan7)
domains (pyhmmer.plan7.Hit attribute)
domZ (pyhmmer.plan7.Pipeline attribute)
E
EaselError
evalue (pyhmmer.plan7.Hit attribute)
F
fd() (pyhmmer.easel.SSIReader.Entry property)
file_info() (pyhmmer.easel.SSIReader method)
find_name() (pyhmmer.easel.SSIReader method)
format() (pyhmmer.easel.SSIReader.FileInfo property)
G
guess_alphabet() (pyhmmer.easel.SequenceFile method)
H
Hit (class in pyhmmer.plan7)
HMM (class in pyhmmer.plan7)
hmm_accession (pyhmmer.plan7.Alignment attribute)
hmm_from (pyhmmer.plan7.Alignment attribute)
hmm_name (pyhmmer.plan7.Alignment attribute)
hmm_sequence (pyhmmer.plan7.Alignment attribute)
hmm_to (pyhmmer.plan7.Alignment attribute)
HMMFile (class in pyhmmer.plan7)
hmmpress() (in module pyhmmer.hmmer)
hmmsearch() (in module pyhmmer.hmmer)
I
i_evalue (pyhmmer.plan7.Domain attribute)
identity_sequence (pyhmmer.plan7.Alignment attribute)
is_local() (pyhmmer.plan7.OptimizedProfile method)
(pyhmmer.plan7.Profile method)
is_multihit() (pyhmmer.plan7.Profile method)
is_sorted() (pyhmmer.plan7.TopHits method)
K
K (pyhmmer.easel.Alphabet attribute)
KeyHash (class in pyhmmer.easel)
Kp (pyhmmer.easel.Alphabet attribute)
L
L (pyhmmer.plan7.Background attribute)
(pyhmmer.plan7.Profile attribute)
M
M (pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.Profile attribute)
module
pyhmmer
pyhmmer.easel
pyhmmer.errors
pyhmmer.hmmer
pyhmmer.plan7
MSA (class in pyhmmer.easel)
N
name (pyhmmer.easel.MSA attribute)
(pyhmmer.easel.Sequence attribute)
(pyhmmer.plan7.Hit attribute)
(pyhmmer.plan7.HMM attribute)
(pyhmmer.plan7.Profile attribute)
name() (pyhmmer.easel.SSIReader.FileInfo property)
nhmmer() (in module pyhmmer.hmmer)
O
optimized() (pyhmmer.plan7.Profile method)
OptimizedProfile (class in pyhmmer.plan7)
P
parse() (pyhmmer.easel.SequenceFile method)
parseinto() (pyhmmer.easel.SequenceFile method)
phmmer() (in module pyhmmer.hmmer)
Pipeline (class in pyhmmer.plan7)
pre_score (pyhmmer.plan7.Hit attribute)
Profile (class in pyhmmer.plan7)
pyhmmer
module
pyhmmer.easel
module
pyhmmer.errors
module
pyhmmer.hmmer
module
pyhmmer.plan7
module
R
read() (pyhmmer.easel.SequenceFile method)
readinto() (pyhmmer.easel.SequenceFile method)
record_length() (pyhmmer.easel.SSIReader.Entry property)
record_offset() (pyhmmer.easel.SSIReader.Entry property)
reverse_complement() (pyhmmer.easel.DigitalSequence method)
(pyhmmer.easel.TextSequence method)
rna() (pyhmmer.easel.Alphabet method)
S
score (pyhmmer.plan7.Domain attribute)
(pyhmmer.plan7.Hit attribute)
search_hmm() (pyhmmer.plan7.Pipeline method)
search_msa() (pyhmmer.plan7.Pipeline method)
search_seq() (pyhmmer.plan7.Pipeline method)
seed (pyhmmer.plan7.Builder attribute)
(pyhmmer.plan7.Pipeline attribute)
Sequence (class in pyhmmer.easel)
sequence (pyhmmer.easel.DigitalSequence attribute)
(pyhmmer.easel.TextSequence attribute)
SequenceFile (class in pyhmmer.easel)
sequences (pyhmmer.easel.DigitalMSA attribute)
(pyhmmer.easel.TextMSA attribute)
set_digital() (pyhmmer.easel.SequenceFile method)
sort() (pyhmmer.plan7.TopHits method)
source (pyhmmer.easel.Sequence attribute)
SSIReader (class in pyhmmer.easel)
SSIReader.Entry (class in pyhmmer.easel)
SSIReader.FileInfo (class in pyhmmer.easel)
SSIWriter (class in pyhmmer.easel)
symbols (pyhmmer.easel.Alphabet attribute)
T
target_from (pyhmmer.plan7.Alignment attribute)
target_name (pyhmmer.plan7.Alignment attribute)
target_sequence (pyhmmer.plan7.Alignment attribute)
target_to (pyhmmer.plan7.Alignment attribute)
textize() (pyhmmer.easel.DigitalMSA method)
(pyhmmer.easel.DigitalSequence method)
TextMSA (class in pyhmmer.easel)
TextSequence (class in pyhmmer.easel)
to_msa() (pyhmmer.plan7.TopHits method)
toggle() (pyhmmer.easel.Bitfield method)
TopHits (class in pyhmmer.plan7)
U
UnexpectedError
W
write() (pyhmmer.easel.MSA method)
(pyhmmer.easel.Sequence method)
(pyhmmer.plan7.HMM method)
(pyhmmer.plan7.OptimizedProfile method)
Z
Z (pyhmmer.plan7.Pipeline attribute)
zero() (pyhmmer.plan7.HMM method)