orange-bioinformatics / _bioinformatics / obiKEGG / types.py

"""
Return types from api classes interface for the SOAP kegg api.

"""

from datetime import datetime
from collections import namedtuple

Definition = namedtuple(
    "Definition", ["entry_id",
                   "definition"
                   ])

def _Definition_from_items(items):
    """ Definition 'items' tuple from a list of items
    """
    items_list = []
    for name, val in items:
        if isinstance(name, list):
            name = name[0]
        if isinstance(val, list):
            val = val[0]
        items_list.append((str(name), str(val)))
    return Definition(**dict(items_list))

Definition.from_items = staticmethod(_Definition_from_items)
    
BInfo = namedtuple(
    'BInfo', ["entry_id",
              "definition",
              "name",
              "release",
              "curator",
              "contents",
              "last_update",
              "supported_formats"
              ])

def _BInfo_from_text(text):
    """ Parse the return string from binfo into a new BInfo instance.
    """
    lines = text.splitlines()
    name, definition = lines[0].split(" ", 1)
    definition = definition.strip()
    
    entry_id, release = lines[1].split(" ", 1)
    _, release = release.strip().split(" ", 1)
    curator = lines[2].strip()
    contents = lines[3].strip()
    _, last_update = lines[4].strip().split(":",1)
    last_update = datetime.strptime(last_update.strip(), "%y/%m/%d").date()
    supported_formats = lines[5].strip()
    return BInfo(entry_id, definition, name, release, curator,
                 contents, last_update, supported_formats)

BInfo.from_text = staticmethod(_BInfo_from_text)


SSDBRelation = namedtuple(
    "SSDBRelation", ["genes_id1",
                     "genes_id2",
                     "sw_score",
                     "bit_score",
                     "identity",
                     "overlap",
                     "start_position1",
                     "end_position1",
                     "start_position2",
                     "end_position2",
                     "best_flag_1to2",
                     "best_flag_2to1",
                     "definition1",
                     "definition2",
                     "length1",
                     "length2"
                     ])

MotifResult = namedtuple(
    "MotifResult", ["motif_id",
                    "definition",
                    "genes_id",
                    "start_position",
                    "end_position",
                    "score",
                    "evalue"
                    ])

LinkDBRelation = namedtuple(
    "LinkDBRelation", ["entry_id1",
                       "entry_id2",
                       "type",
                       "path"
                       ])

PathwayElement = namedtuple(
    "PathwayElement", ["element_id",
                       "type",
                       "names",
                       "components"
                       ])

PathwayElementRelation = namedtuple(
    "PathwayElementRelation", ["element_id1",
                               "element_id2",
                               "type",
                               "subtypes"
                               ])

Subtype = namedtuple(
    "Subtype", ["element_id",
                "relation",
                "type",
                ])
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