Python Service.get_template方法代码示例

# 需要导入模块: from intermine.webservice import Service [as 别名]
# 或者: from intermine.webservice.Service import get_template [as 别名]
def fetchGene(GeneName):
    
    service = Service("http://yeastmine.yeastgenome.org/yeastmine/service")
    template = service.get_template('Gene_GenomicDNA')

    rows = template.rows(
        E = {"op": "LOOKUP", "value": GeneName, "extra_value": "S. cerevisiae"}
    )
    
    # this service seems to return multiple similar genes but we want the first one only, so count
    # and it returns information about the gene you want
    count=0
    for row in rows:
        
        count=count+1
        if count==1:
            descr= row["description"]
            GeneSeq=Seq(row["sequence.residues"])
            GeneSysName=row["secondaryIdentifier"]
       
    #let's create a record for the oldGene
    GeneRecord = SeqRecord(GeneSeq, id=GeneSysName)
    
    #now let's add some more information to make it useful
    GeneRecord.name=GeneName
    GeneRecord.features=GeneSysName
    GeneRecord.description=descr

    return GeneRecord 

# 需要导入模块: from intermine.webservice import Service [as 别名]
# 或者: from intermine.webservice.Service import get_template [as 别名]
def fetchGene(GeneName):
    
    service = Service("http://yeastmine.yeastgenome.org/yeastmine/service")
    template = service.get_template('Gene_GenomicDNA')

    rows = template.rows(
        E = {"op": "LOOKUP", "value": GeneName, "extra_value": "S. cerevisiae"}
    )
    
    # this service seems to return multiple similar genes but we want the first one only, so count
    # and it returns information about the gene you want
    count=0
    for row in rows:
        
        count=count+1
        if count==1:
            descr= row["description"]
            GeneSeq=Seq(row["sequence.residues"])
            GeneSysName=row["secondaryIdentifier"]
            print(" ")
            print("I think you want...... "+row["secondaryIdentifier"])
            print(row["description"])
            print(" ")
            print(row["sequence.residues"])
            print(" ")
            print("Good choice! I have a feeling you're going to get lucky with this one.")
            print(" ")
            print("Give me a second to put some of my ducks in a circle...")
       

            
    #let's create a record for the oldGene
    GeneRecord = SeqRecord(GeneSeq, id=GeneSysName)
    
    #now let's add some more information to make it useful
    GeneRecord.name=GeneName
    GeneRecord.features=GeneSysName

    return GeneRecord

# 需要导入模块: from intermine.webservice import Service [as 别名]
# 或者: from intermine.webservice.Service import get_template [as 别名]
import pandas as pd

service = Service("http://yeastmine.yeastgenome.org/yeastmine/service")

#-------------------------------------------------------------------#
# Gene Info
#-------------------------------------------------------------------# 
gene = service.model.Gene.where(symbol = 'HFA1').first()

print gene.symbol + "\n" + gene.description
print gene

#-------------------------------------------------------------------#
# Model templates
#-------------------------------------------------------------------#
template = service.get_template("Gene_Pathways")
for row in template.results(A={"symbol":"HFA1"}):
	print row

#-------------------------------------------------------------------#
# Query
#-------------------------------------------------------------------#
query = service.new_query("Gene")
query.add_view("primaryIdentifier","name","symbol","pathways.name")
query.add_constraint("Gene", "LOOKUP", "HFA1")
for row in query.rows():
	print row

# The view specifies the output columns
query.add_view(
    "primaryIdentifier", "secondaryIdentifier", "symbol", "name", "sgdAlias",

# 需要导入模块: from intermine.webservice import Service [as 别名]
# 或者: from intermine.webservice.Service import get_template [as 别名]
def get_protein_seq_as_FASTA(gene_id, 
    extension_for_saving = extension_for_saving, return_text = False):
    '''
    Main function of script. 
    Takes a gene's systematic name, standard name, or alias as defined at gene 
    page at yeastgenome.org, retrieves the associated information from 
    YeastMine, and saves or returns the protein sequence in FASTA format.

    Use `return_text` if calling from IPython or a Jupyter notebook and you want
    the FASTA record returned as text,
    '''
    # Get gene information from YeastMine
    #---------------------------------------------------------------------------
    # Based on the template Gene_ProteinSequence available under 
    # 'Gene --> Protein Sequence' when clicking on 'Proteins' on navigation bar 
    # in middle of page at YeastMine. Direct link:
    # https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinSequence&scope=global
    
    service = Service("https://yeastmine.yeastgenome.org:443/yeastmine/service")

    # Retrieve protein sequence for a specified gene.

    template = service.get_template('Gene_ProteinSequence')

    # You can edit the constraint values below
    # B    Gene

    rows = template.rows(
        B = {"op": "LOOKUP", "value": gene_id, "extra_value": "S. cerevisiae"}
    )
    results = []
    for row in rows:
        results.append(row)
    
    # store corresponding protein sequence
    prot_seq = results[0]["proteins.sequence.residues"]
    
    # format gene_nom_info for making output file name or anything else needing 
    # that information
    gene_nom_info = {}
    gene_nom_info['sys_nom'] = results[0]["secondaryIdentifier"]
    gene_nom_info['std_nom'] = results[0]["symbol"]
    gene_nom_info['aliases'] = results[0]["sgdAlias"]
    #print (gene_nom_info['aliases'] ) # FOR DEBUGGING ONLY
    #print (gene_nom_info['std_nom'] ) # FOR DEBUGGING ONLY
    #print (gene_nom_info['sys_nom'] ) # FOR DEBUGGING ONLY


    # feedback
    sys.stderr.write("looking up the gene associated with "
        "{}...".format(gene_id))


    # Make output FASTA record
    #---------------------------------------------------------------------------
    # based handling worked out in 
    # `delete_seq_following_pattern_within_multiFASTA.py`
    record_description = '{}'.format(gene_nom_info['sys_nom'])
    record = SeqRecord(Seq(prot_seq, generic_protein), 
            id=gene_nom_info['std_nom'], description=record_description)#based
        # on https://www.biostars.org/p/48797/ and `.ungap()` method, see
        # https://github.com/biopython/biopython/issues/1511 , and `description`
        # from what I've seen for `id` plus https://biopython.org/wiki/SeqIO
        #print (records[indx]) # ONLY FOR DEBUGGING
    sys.stderr.write("getting protein sequence...")

    # Return text if called with `return_text = True`. Otherwise, consider 
    # called from command line & save file.
    #---------------------------------------------------------------------------
    if return_text == True:
        # based on section 4.6 at 
        #http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec:SeqRecord-format
        # Feedback
        sys.stderr.write("\nReturning protein sequence in FASTA format.")
        return record.format("fasta") 
    else:
        output_file_name = generate_output_file_name(
            gene_nom_info,extension_for_saving)
        SeqIO.write(record,output_file_name, "fasta");
        # Feedback
        sys.stderr.write("\n\nFile of protein sequence "
            "saved as '{}'.".format(output_file_name))
        sys.stderr.write("\nFinished.\n")

# 需要导入模块: from intermine.webservice import Service [as 别名]
# 或者: from intermine.webservice.Service import get_template [as 别名]
#
# Saccharomyces Genome Database (SGD)
# http://yeastmine.yeastgenome.org/yeastmine/api.do?subtab=python
#
# YeastMine example script
#

from intermine.webservice import Service

service = Service("http://yeastmine.yeastgenome.org/yeastmine/service")

# List all GO annotations for a specified gene. Searches for the
# primaryIdentifier (SGDID), secondaryIdentifier (Systematic Name), symbol
# (Standard Gene Name) and wild card queries (such as *YAL*) are supported. 
# Manually curated, high-throughput, and computational GO annotations are
# included. Genes include Uncharacterized and Verified ORFs, pseudogenes,
# transposable element genes, RNAs, and genes Not in Systematic Sequence of
# S228C.

template = service.get_template('Gene_GO')

# You can edit the constraint values below
# A    Gene    Show GO annotations for gene:

rows = template.rows(
				A = {"op": "LOOKUP", "value": "YAL018C", "extra_value": "S. cerevisiae"}
				)
for row in rows:
	print row