cls.MITABAccess Namespace Reference

Class for accessing the interaction data from MITAB files. More...

Classes
class	CMitabParserParams
class	CMITABAccess
	Parses and stores the content of a MITAB file for later querying. More...

Variables
list	MITAB_COLS
string	MITAB_EMPTY = "-"
string	MITAB_DELIM = "|"
string	MITAB_DELIM_2 = ":"
string	TOKEN_MICV_GENE_ID = "entrezgene/locuslink"
string	TOKEN_MICV_UNIPROT = "uniprotkb"
string	TOKEN_MICV_REFSEQ = "refseq"
string	TOKEN_IN_GENE_ID = "entrez"
string	TOKEN_IN_UNIPROT = "uniprot"
string	TOKEN_IREF_COMPLEX = "complex"
string	TOKEN_PPI = "ppi"
string	TOKEN_SELF = "self"
string	TOKEN_COMPLEX = "complex"
string	TOKEN_ROGID = "rogid"
string	TOKEN_IREFINDEX = "irefindex"
list	SUPPORTED_INPUTS = [TOKEN_IN_UNIPROT, TOKEN_IN_GENE_ID]
list	SUPPORTED_INTERACTION_TYPES = [TOKEN_PPI, TOKEN_SELF, TOKEN_COMPLEX]
list	EMPTY_CELL = ["-", "", "--"]
dictionary	MI_CV_PREDICTION
list	DEFAULT_DATA_TYPE = [TOKEN_PPI]
bool	DEFAULT_INCLUDE_PREDICTIONS = False
bool	DEFAULT_INCLUDE_NON_HUMAN = False
bool	DEFAULT_MAP_IDENTIFIERS = False
int	DEFAULT_MAX_COMPLEX_LENGTH = 1000

Detailed Description

Class for accessing the interaction data from MITAB files.

Authors

Hagen Blankenburg

Date

2013-10-12

Copyright

See LICENSE file.

Variable Documentation

DEFAULT_DATA_TYPE

list cls.MITABAccess.DEFAULT_DATA_TYPE = [TOKEN_PPI]

DEFAULT_INCLUDE_NON_HUMAN

bool cls.MITABAccess.DEFAULT_INCLUDE_NON_HUMAN = False

DEFAULT_INCLUDE_PREDICTIONS

bool cls.MITABAccess.DEFAULT_INCLUDE_PREDICTIONS = False

DEFAULT_MAP_IDENTIFIERS

bool cls.MITABAccess.DEFAULT_MAP_IDENTIFIERS = False

DEFAULT_MAX_COMPLEX_LENGTH

int cls.MITABAccess.DEFAULT_MAX_COMPLEX_LENGTH = 1000

EMPTY_CELL

list cls.MITABAccess.EMPTY_CELL = ["-", "", "--"]

MI_CV_PREDICTION

dictionary cls.MITABAccess.MI_CV_PREDICTION

Initial value:

=  {
    "MI:0063" : "interaction prediction",
    "MI:0046" : "experimental knowledge based",
    "MI:0037" : "domain profile pairs",
    "MI:0064" : "interologs mapping",
    "MI:0110" : "text mining",
    "MI:0024" : "confirmational text mining",
    "MI:0087" : "predictive text mining",
    "MI:0058" : "genome based prediction",
    "MI:0036" : "domain fusion",
    "MI:0057" : "gene neighbourhood",
    "MI:0085" : "phylogenetic profile",
    "MI:0100" : "sequence based phylogenetic profile",
    "MI:1177" : "phylogenetic profiling of predicted gene regulatory region \
    binding site",
    "MI:0101" : "sequence based prediction",
    "MI:0026" : "correlated mutations",
    "MI:0036" : "domain fusion",
    "MI:0037" : "domain profile pairs",
    "MI:0064" : "interologs mapping",
    "MI:1178" : "sequence based prediction of binding of transcription factor \
    to transcribed gene regulatory elements",
    "MI:1176" : "sequence based prediction of gene regulatory region binding \
    sites",
    "MI:0105" : "structure based prediction",
    "MI:0035" : "docking"
}

MITAB_COLS

list cls.MITABAccess.MITAB_COLS

Initial value:

=  [{"i": 10, "id": "taxA", "full": "Taxonomy A"},
         {"i": 11, "id": "taxB", "full": "Taxonomy B"},
         {"i": 7, "id": "detectionMethod", "full": "Detection method"},
         {"i": 1, "id": "idA", "full": "Unique ID A"},
         {"i": 2, "id": "idB", "full": "Unique ID B"},
         {"i": 3, "id": "altA", "full": "Alterantive ID A"},
         {"i": 4, "id": "altB", "full": "Alternative ID B"},
         {"i": 5, "id": "aliasA", "full": "Alias A"},
         {"i": 6, "id": "aliasB", "full": "Alias B"},
         {"i": 8, "id": "author", "full": "Author"},
         {"i": 9, "id": "pubmed", "full": "PubMed ID"},
         {"i": 12, "id": "interactionType", "full": "Interaction Type"},
         {"i": 13, "id": "sourceDB", "full": "Source DB"},
         {"i": 14, "id": "interactionId", "full": "Interaction ID"},
         {"i": 15, "id": "confidence", "full": "Confidence"}]

MITAB_DELIM

string cls.MITABAccess.MITAB_DELIM = "|"

MITAB_DELIM_2

string cls.MITABAccess.MITAB_DELIM_2 = ":"

MITAB_EMPTY

string cls.MITABAccess.MITAB_EMPTY = "-"

SUPPORTED_INPUTS

list cls.MITABAccess.SUPPORTED_INPUTS = [TOKEN_IN_UNIPROT, TOKEN_IN_GENE_ID]

SUPPORTED_INTERACTION_TYPES

list cls.MITABAccess.SUPPORTED_INTERACTION_TYPES = [TOKEN_PPI, TOKEN_SELF, TOKEN_COMPLEX]

TOKEN_COMPLEX

string cls.MITABAccess.TOKEN_COMPLEX = "complex"

TOKEN_IN_GENE_ID

string cls.MITABAccess.TOKEN_IN_GENE_ID = "entrez"

TOKEN_IN_UNIPROT

string cls.MITABAccess.TOKEN_IN_UNIPROT = "uniprot"

TOKEN_IREF_COMPLEX

string cls.MITABAccess.TOKEN_IREF_COMPLEX = "complex"

TOKEN_IREFINDEX

string cls.MITABAccess.TOKEN_IREFINDEX = "irefindex"

TOKEN_MICV_GENE_ID

string cls.MITABAccess.TOKEN_MICV_GENE_ID = "entrezgene/locuslink"

TOKEN_MICV_REFSEQ

string cls.MITABAccess.TOKEN_MICV_REFSEQ = "refseq"

TOKEN_MICV_UNIPROT

string cls.MITABAccess.TOKEN_MICV_UNIPROT = "uniprotkb"

TOKEN_PPI

string cls.MITABAccess.TOKEN_PPI = "ppi"

TOKEN_ROGID

string cls.MITABAccess.TOKEN_ROGID = "rogid"

TOKEN_SELF

string cls.MITABAccess.TOKEN_SELF = "self"