integron

class integron_finder.integron.Integron(replicon, cfg)

Integron object represents an object composed of an integrase, attC sites and gene cassettes. Each element is characterized by their coordinates in the replicon, the strand (+ or -), the ID of the gene (except attC). The object Integron is also characterized by the ID of the replicon.

__init__(replicon, cfg)

Parameters:

• replicon (a Bio.Seq.SeqRecord object) – The replicon where integrons has been found
• cfg (a integron_finder.config.Config object) – the configuration

__weakref__

list of weak references to the object (if defined)

add_attC(pos_beg_attC, pos_end_attC, strand, evalue, model)

Adds attC site to the Integron object.

Parameters:

• pos_beg_attC (int) – the position on the replicon of the beginning attc site
• pos_end_attC (int) – the position on replicon of the end of the attc site
• strand (int) – the strand where is found the attc 1 for forward, -1 for reverse
• evalue (float) – the evalue associated to this attc site
• model (str) – the name of attc model (for instance attc4)

add_attI()

Looking for Att1 sites and add them to this integron.

add_integrase(pos_beg_int, pos_end_int, id_int, strand_int, evalue, model)

Adds integrases to the integron. Should be called once.

Parameters:

• pos_beg_int (int) – the position on the replicon of the beginning integrase site
• pos_end_int (int) – the position on replicon of the end of the integrase site
• id_int (str) – The protein id corresponding to the integrase
• strand_int (int) – the strand where is found the attc 1 for forward, -1 for reverse
• evalue (float) – the evalue associated to this attc site
• model (str) – the name of integrase model (for instance intersection_tyr_intI)

add_promoter()

Looks for known promoters if they exists within your integrons element. It takes 1s for about 13kb.

add_proteins(prot_db)

Parameters:prot_db (integron.prot_db.ProteinDB object.) – The protein db corresponding to the translation of the replicon

describe()

Returns:DataFrame describing the integron object The columns are:

”pos_beg”, “pos_end”, “strand”, “evalue”, “type_elt”, “model”, “distance_2attC”, “annotation”, “considered_topology”

draw_integron(file=None)

Represent the different element of the integrons if file is provide save the drawing on the file otherwise display it on screen.

Parameters:file (str) – the path to save the integron schema (in pdf format)

has_attC()

Returns:True if integron has attc sites False otherwise.

has_integrase()

Returns:True if integron has integrase False otherwise.

type()

Returns:The type of the integrons:

• ’complete’ : Have one integrase and at least one attC
• ’CALIN’ : Have at least one attC
• ’In0’ : Just an integrase intI

Return type:str

integron_finder.integron.find_integron(replicon, prot_db, attc_file, intI_file, phageI_file, cfg)

Function that looks for integrons given rules :

• presence of intI
• presence of attC
• d(intI-attC) <= 4 kb
• d(attC-attC) <= 4 kb

It returns the list of all integrons, be they complete or not. found in attC files + integrases file which are formatted as follow : intI_file : Accession_number ID_prot strand pos_beg pos_end evalue attc_file : Accession_number attC cm_debut cm_fin pos_beg pos_end sens evalue

Parameters:

• replicon (Bio.Seq.SeqRecord object) – the name of the replicon
• prot_db (a integron_finder.prot_db.ProteinDB object.) – the protein database corresponding to the replicon translation
• attc_file (path to cmsearch output or pd.Dataframe) – the output of cmsearch or the result of parsing of this file by read_infernal
• intI_file (str) – the output of hmmsearch with the integrase model
• phageI_file (str) – the output of hmmsearch with the phage model
• cfg (a integron_finder.config.Config object) – configuration

Returns:

list of all integrons, be they complete or not

Retype:

list of Integron object