prot_db

The prot_db module contains classes to handle protein file and protein description which can be either generate by Prodigal or Provide by Gembase. It also provide an interface to abstract the way to get protein sequences and descriptions

class integron_finder.prot_db.ProteinDB(replicon, cfg, prot_file=None)

AbstractClass defining the interface for ProteinDB. ProteinDB provide an abstraction and a way to access to proteins corresponding to the replicon/contig CDS.

__getitem__(prot_seq_id)

Parameters:prot_seq_id (str) – the id of a protein sequence Returns:The Sequence corresponding to the prot_seq_id. Return type:Bio.SeqRecord object Raises:KeyError – when seq_id does not match any sequence in DB

__init__(replicon, cfg, prot_file=None)

Initialize self. See help(type(self)) for accurate signature.

__iter__()

Returns:a generator which iterate on the protein seq_id which constitute the contig. Return type:generator

__weakref__

list of weak references to the object (if defined)

_make_db()

Returns:an index of the sequence contains in protfile corresponding to the replicon

_make_protfile()

Create fasta file with protein corresponding to the nucleic sequence (replicon)

Returns:the path of the created protein file Return type:str

get_description(gene_id)

Parameters:

gene_id (str) – a protein/gene identifier

Returns:

The description of the protein corresponding to the gene_id

Return type:

SeqDesc namedtuple object

Raises:

• IntegronError – when gene_id is not a valid Gembase gene identifier
• KeyError – if gene_id is not found in GembaseDB instance

protfile

Returns:The absolute path to the protein file corresponding to contig id Return type:str

class integron_finder.prot_db.ProdigalDB(replicon, cfg, prot_file=None)

Creates proteins from Replicon/contig using prodigal and provide facilities to access them.

__getitem__(prot_seq_id)

Parameters:prot_seq_id (str) – the id of a protein sequence Returns:The Sequence corresponding to the prot_seq_id. Return type:Bio.SeqRecord object

__iter__()

Returns:a generator which iterate on the protein seq_id which constitute the contig. Return type:generator

_make_protfile()

Use prodigal to generate proteins corresponding to the replicon

Returns:the path of the created protfile Return type:str

get_description(gene_id)

Parameters:

gene_id (str) – a protein/gene identifier

Returns:

The description of the protein corresponding to the gene_id

Return type:

SeqDesc namedtuple object

Raises:

• IntegronError – when gene_id is not a valid Gembase gene identifier
• KeyError – if gene_id is not found in ProdigalDB instance

class integron_finder.prot_db.GembaseDB(replicon, cfg, prot_file=None)

Implements ProteinDB from a Gembase. Managed proteins from Proteins directory corresponding to a replicon/contig

__getitem__(prot_seq_id)

Parameters:prot_seq_id (str) – the id of a protein sequence Returns:The Sequence corresponding to the prot_seq_id. Return type:Bio.SeqRecord object

__init__(replicon, cfg, prot_file=None)

Initialize self. See help(type(self)) for accurate signature.

__iter__()

Returns:a generator which iterate on the protein seq_id which constitute the contig. Return type:generator

_make_protfile()

Create fasta file with protein corresponding to this sequence, from the corresponding Gembase protfile This step is necessary because in Gembase Draft One nucleic file can contains several contigs, but all proteins are in the same file.

Returns:the path of the created protein file Return type:str

_parse_lst()

Parse the LSTINFO file and extract information specific to the replicon :return:

static gembase_complete_parser(lst_path, sequence_id)

Parameters:

• lst_path (str) – the path of of the LSTINFO file Gembase Complet
• sequence_id (str) – the id of the genomic sequence to analyse

Returns:

the information related to the ‘valid’ CDS corresponding to the sequence_id

Return type:

class:pandas.DataFrame` object

static gembase_draft_parser(lst_path, replicon_id)

Parameters:

• lst_path (str) – the path of of the LSTINFO file from a Gembase Draft
• sequence_id (str) – the id of the genomic sequence to analyse

Returns:

the information related to the ‘valid’ CDS corresponding to the sequence_id

Return type:

class:pandas.DataFrame` object

static gembase_sniffer(lst_path)

Detect the type of gembase :param str lst_path: the path to the LSTINFO file corresponding to the nucleic sequence :returns: either ‘Complet’ or ‘Draft’

get_description(gene_id)

Parameters:

gene_id (str) – a protein/gene identifier

Returns:

The description of the protein corresponding to the gene_id

Return type:

SeqDesc namedtuple object

Raises:

• IntegronError – when gene_id is not a valid Gembase gene identifier
• KeyError – if gene_id is not found in GembaseDB instance

class integron_finder.prot_db.SeqDesc(id, strand, start, stop)

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

static __new__(_cls, id, strand, start, stop)

Create new instance of SeqDesc(id, strand, start, stop)

__repr__()

Return a nicely formatted representation string

_asdict()

Return a new OrderedDict which maps field names to their values.

classmethod _make(iterable)

Make a new SeqDesc object from a sequence or iterable

_replace(**kwds)

Return a new SeqDesc object replacing specified fields with new values

id

Alias for field number 0

start

Alias for field number 2

stop

Alias for field number 3

strand

Alias for field number 1