IntegronFinder
2.0
User Guide
Introduction
Installation
IntegronFinder dependencies
Installation procedure
From Version 2.0
From Version 1.5.1 and after
For Version 1.5 and before
Uninstallation procedure
From Version 1.5.1 and after
From Version 1.0 to Version 1.5
How to install Python
What’s new ?
In Version 2.0
Quick start
For impatient
Input and Outputs
Inputs
Outputs
For everyone
Thorough local detection
CALIN detection
Functional annotation
Search for promoter and
attI
sites
Keep intermediate results
Topology
For big data people
Parallelization
For integron diggers
Clustering of elements
Integrase
attC
evalue
attC
size
Palindromes
attC
alignements
web server
Galaxy
How to use it
Results
References
Developer Guide
Developer installation
Build a new release
Send changes to upstream repository
Tests
Running tests
Adding tests
Documentation
Architecture Overview
Project files and directories
Files
Directories
Technical overview
Integron_finder API Reference
annotation
attc
config
hmm
infernal
integrase
integron
prot_db
results
topology
utils
IntegronFinder
»
Index
Index
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A
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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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L
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M
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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
_
__getitem__() (integron_finder.prot_db.GembaseDB method)
(integron_finder.prot_db.ProdigalDB method)
(integron_finder.prot_db.ProteinDB method)
(integron_finder.topology.Topology method)
__getnewargs__() (integron_finder.prot_db.SeqDesc method)
__init__() (integron_finder.config.Config method)
(integron_finder.integron.Integron method)
(integron_finder.prot_db.GembaseDB method)
(integron_finder.prot_db.ProteinDB method)
(integron_finder.topology.Topology method)
(integron_finder.utils.FastaIterator method)
__iter__() (integron_finder.prot_db.GembaseDB method)
(integron_finder.prot_db.ProdigalDB method)
(integron_finder.prot_db.ProteinDB method)
__len__() (integron_finder.utils.FastaIterator method)
__new__() (integron_finder.prot_db.SeqDesc static method)
__next__() (integron_finder.utils.FastaIterator method)
__repr__() (integron_finder.prot_db.SeqDesc method)
__weakref__ (integron_finder.config.Config attribute)
(integron_finder.integron.Integron attribute)
(integron_finder.prot_db.ProteinDB attribute)
(integron_finder.topology.Topology attribute)
(integron_finder.utils.FastaIterator attribute)
_asdict() (integron_finder.prot_db.SeqDesc method)
_check_seq_alphabet_compliance() (integron_finder.utils.FastaIterator method)
_find_gembase_file_basename() (integron_finder.prot_db.GembaseDB method)
_log (in module integron_finder.results)
_make() (integron_finder.prot_db.SeqDesc class method)
_make_db() (integron_finder.prot_db.ProteinDB method)
_make_protfile() (integron_finder.prot_db.GembaseDB method)
(integron_finder.prot_db.ProdigalDB method)
(integron_finder.prot_db.ProteinDB method)
_parse() (integron_finder.topology.Topology method)
_parse_lst() (integron_finder.prot_db.GembaseDB method)
_parse_topology() (integron_finder.topology.Topology method)
_replace() (integron_finder.prot_db.SeqDesc method)
_set_topologies() (integron_finder.utils.FastaIterator method)
A
add_attC() (integron_finder.integron.Integron method)
add_attI() (integron_finder.integron.Integron method)
add_feature() (in module integron_finder.annotation)
add_integrase() (integron_finder.integron.Integron method)
add_promoter() (integron_finder.integron.Integron method)
add_proteins() (integron_finder.integron.Integron method)
C
Config (class in integron_finder.config)
D
default_topology() (integron_finder.config.Config property)
describe() (integron_finder.integron.Integron method)
draw_integron() (integron_finder.integron.Integron method)
E
expand() (in module integron_finder.infernal)
F
FastaIterator (class in integron_finder.utils)
filter_calin() (in module integron_finder.results)
find_attc() (in module integron_finder.infernal)
find_attc_max() (in module integron_finder.attc)
find_integrase() (in module integron_finder.integrase)
find_integron() (in module integron_finder.integron)
func_annot() (in module integron_finder.annotation)
func_annot_path() (integron_finder.config.Config property)
G
gembase_complete_parser() (integron_finder.prot_db.GembaseDB static method)
gembase_draft_parser() (integron_finder.prot_db.GembaseDB static method)
gembase_sniffer() (integron_finder.prot_db.GembaseDB static method)
GembaseDB (class in integron_finder.prot_db)
get_description() (integron_finder.prot_db.GembaseDB method)
(integron_finder.prot_db.ProdigalDB method)
(integron_finder.prot_db.ProteinDB method)
get_name_from_path() (in module integron_finder.utils)
H
has_attC() (integron_finder.integron.Integron method)
has_integrase() (integron_finder.integron.Integron method)
I
id (integron_finder.prot_db.SeqDesc attribute)
input_dir() (integron_finder.config.Config property)
input_seq_path() (integron_finder.config.Config property)
Integron (class in integron_finder.integron)
integron_finder.annotation
module
integron_finder.attc
module
integron_finder.config
module
integron_finder.hmm
module
integron_finder.infernal
module
integron_finder.integrase
module
integron_finder.integron
module
integron_finder.prot_db
module
integron_finder.results
module
integron_finder.topology
module
integron_finder.utils
module
integrons_report() (in module integron_finder.results)
L
local_max() (in module integron_finder.infernal)
log_level() (in module integron_finder.utils)
(integron_finder.config.Config property)
M
make_multi_fasta_reader() (in module integron_finder.utils)
merge_results() (in module integron_finder.results)
model_attc_name() (integron_finder.config.Config property)
model_attc_path() (integron_finder.config.Config property)
model_dir() (integron_finder.config.Config property)
model_integrase() (integron_finder.config.Config property)
model_len() (in module integron_finder.utils)
(integron_finder.config.Config property)
model_phage_int() (integron_finder.config.Config property)
module
integron_finder.annotation
integron_finder.attc
integron_finder.config
integron_finder.hmm
integron_finder.infernal
integron_finder.integrase
integron_finder.integron
integron_finder.prot_db
integron_finder.results
integron_finder.topology
integron_finder.utils
O
outdir() (integron_finder.config.Config property)
P
ProdigalDB (class in integron_finder.prot_db)
ProteinDB (class in integron_finder.prot_db)
protfile() (integron_finder.prot_db.ProteinDB property)
R
read_hmm() (in module integron_finder.hmm)
read_infernal() (in module integron_finder.infernal)
read_multi_prot_fasta() (in module integron_finder.utils)
result_dir() (integron_finder.config.Config property)
S
scan_hmm_bank() (in module integron_finder.hmm)
search_attc() (in module integron_finder.attc)
SeqDesc (class in integron_finder.prot_db)
start (integron_finder.prot_db.SeqDesc attribute)
stop (integron_finder.prot_db.SeqDesc attribute)
strand (integron_finder.prot_db.SeqDesc attribute)
summary() (in module integron_finder.results)
T
tmp_dir() (integron_finder.config.Config method)
Topology (class in integron_finder.topology)
type() (integron_finder.integron.Integron method)