How to use the bioservices.KEGG function in bioservices

To help you get started, we’ve selected a few bioservices examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github cokelaer / bioservices / test / test_kegg.py View on Github external
def kegg():
    k = KEGG()
    k.organismIds
    k.organism = "hsa"
    return k
github sys-bio / tellurium / tellurium / notebooks / ontologysearch.py View on Github external
def __init__(self):
        self.ch = bioservices.ChEBI()
        self.kegg = bioservices.KEGG()

        self.wOntologySelect = w.Dropdown(description='Ontology:', options=['ChEBI', 'KEGG.Reaction'])
        self.wSearchTerm = w.Text(description='Search Term:', value="glucose")
        self.wSearchTerm.on_submit(self.search)
        self.wSearchButton = w.Button(description='Search')
        self.wSearchButton.on_click(self.search)

        self.wResultsSelect = w.Select(description='Results:', width='100%')
        self.wResultsSelect.on_trait_change(self.selectedTerm)
        self.wResultsURL = w.Textarea(description='URL:', width='100%')
        self.wResults = w.VBox(children=[
                self.wResultsSelect,
                self.wResultsURL
        ], width='100%')
        for ch in self.wResults.children:
            ch.font_family = 'monospace'
github sequana / sequana / sequana / enrichment.py View on Github external
def __init__(self, folder, organism, comparison=None, alpha=0.05, fc=0):
        print("DRAFT in progress")
        from bioservices import KEGG
        self.kegg = KEGG(cache=True)
        self.kegg.organism = organism

        self.read_rnadiff(folder, alpha=alpha, fc=fc)
        choices = list(self.rnadiff.dr_gene_lists.keys())
        if comparison:
            assert comparison in choices
            self.comparison = comparison
        elif len(choices) == 1:
            logger.info("One comparison found and set automatically")
            self.comparison = choices[0]

        self.background = len(self.kegg.list(self.kegg.organism).split("\n"))
        logger.info("Set number of genes to {}".format(self.background))

        self._load_pathways()
github SBRG / ssbio / ssbio / databases / kegg.py View on Github external
"""

import io
import logging
import os.path as op
from collections import defaultdict

from bioservices import KEGG
from slugify import Slugify

import ssbio.utils
from ssbio.protein.sequence.seqprop import SeqProp

log = logging.getLogger(__name__)
custom_slugify = Slugify(safe_chars='-_')
bs_kegg = KEGG()


class KEGGProp(SeqProp):
    def __init__(self, seq, id, name='', description='',
                 fasta_path=None, txt_path=None, gff_path=None):
        SeqProp.__init__(self, id=id, seq=seq, name=name, description=description,
                         sequence_path=fasta_path, metadata_path=txt_path, feature_path=gff_path)
        self.kegg = id

    @SeqProp.metadata_path.setter
    def metadata_path(self, m_path):
        """Provide pointers to the paths of the metadata file

        Args:
            m_path: Path to metadata file
github SBRG / ssbio / ssbio / pipeline / gempro.py View on Github external
from ssbio.databases.kegg import KEGGProp
from ssbio.databases.uniprot import UniProtProp
from ssbio.protein.sequence.properties.scratch import SCRATCH

if utils.is_ipynb():
    from tqdm import tqdm_notebook as tqdm
else:
    from tqdm import tqdm

custom_slugify = Slugify(safe_chars='-_.')
logging.getLogger("requests").setLevel(logging.ERROR)
logging.getLogger("urllib3").setLevel(logging.ERROR)
log = logging.getLogger(__name__)
date = utils.Date()
bs_unip = UniProt()
bs_kegg = KEGG()


class GEMPRO(Object):

    """Generic class to represent all information for a GEM-PRO project.

    Initialize the GEM-PRO project with a genome-scale model, a list of genes, or a dict of genes and sequences.
    Specify the name of your project, along with the root directory where a folder with that name will be created.

    Main methods provided are:

    #. Automated mapping of sequence IDs

        * With KEGG mapper
        * With UniProt mapper
        * Allowing manual gene ID --> protein sequence entry