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Index
A
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B
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C
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F
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G
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I
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J
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K
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L
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M
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N
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P
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Q
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R
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S
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T
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U
A
abtools._compare (module)
abtools._finder (module)
abtools._phylogeny (module)
abtools.alignment (module)
abtools.cluster (module)
abtools.log (module)
abtools.mongodb (module)
abtools.pipeline (module)
abtools.s3 (module)
abtools.sequence (module)
aggregate() (in module abtools._compare)
aligned_query (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
aligned_target (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
alignment_midline (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
alignment_type (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
B
BaseAlignment (class in abtools.alignment)
bc_similarity() (in module abtools._compare)
C
centroid (abtools.cluster.Cluster attribute)
chunker() (in module abtools._finder)
Cluster (class in abtools.cluster)
cluster() (in module abtools.cluster)
compress() (in module abtools.s3)
compress_and_upload() (in module abtools.s3)
configure() (in module abtools.s3)
consensus (abtools.cluster.Cluster attribute)
cosine_similarity() (in module abtools._compare)
F
fasta (abtools.sequence.Sequence attribute)
fastq (abtools.sequence.Sequence attribute)
G
get_collections() (in module abtools.mongodb)
get_connection() (in module abtools.mongodb)
get_db() (in module abtools.mongodb)
get_logger() (in module abtools.log)
global_alignment() (in module abtools.alignment)
I
ids (abtools.cluster.Cluster attribute)
index() (in module abtools.mongodb)
initialize() (in module abtools.pipeline)
J
jaccard_similarity() (in module abtools._compare)
js_similarity() (in module abtools._compare)
K
kl_divergence() (in module abtools._compare)
L
list_files() (in module abtools.pipeline)
local_alignment() (in module abtools.alignment)
M
mafft() (in module abtools.alignment)
make_dir() (in module abtools.pipeline)
mh_similarity() (in module abtools._compare)
mongoimport() (in module abtools.mongodb)
muscle() (in module abtools.alignment)
N
NWAlignment (class in abtools.alignment)
P
put() (in module abtools.s3)
Q
query (abtools.alignment.BaseAlignment attribute)
query_begin (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
query_end (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
R
raw_query (abtools.alignment.BaseAlignment attribute)
raw_target (abtools.alignment.BaseAlignment attribute)
region() (abtools.sequence.Sequence method)
remove_padding() (in module abtools.mongodb)
rename_collection() (in module abtools.mongodb)
renkonen_similarity() (in module abtools._compare)
reverse_complement (abtools.sequence.Sequence attribute)
run() (in module abtools._compare)
(in module abtools._finder)
(in module abtools._phylogeny)
S
score (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
sd_similarity() (in module abtools._compare)
Sequence (class in abtools.sequence)
sequences (abtools.cluster.Cluster attribute)
setup_logging() (in module abtools.log)
shannon_entropy() (in module abtools._compare)
size (abtools.cluster.Cluster attribute)
SSWAlignment (class in abtools.alignment)
T
target (abtools.alignment.BaseAlignment attribute)
target_begin (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
target_end (abtools.alignment.NWAlignment attribute)
(abtools.alignment.SSWAlignment attribute)
target_id (abtools.alignment.BaseAlignment attribute)
U
unset() (in module abtools.mongodb)
update() (in module abtools.mongodb)
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