Entrez loop errors
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Entering edit mode
2.1 years ago

Hey all I am trying to create a data base but I am having some issues. My below code is running but it is only pulling the last enzyme glucose-6-phosphate dehydrogenase into the table (and its subunits, etc.) and I am not sure why. Any help would be appreciated, thanks!

import sqlite3
#creating connection to my.db
conn = sqlite3.connect ('my.db')
c = conn.cursor()

#creation of genes table
c.execute("""CREATE TABLE genes (id INTEGER PRIMARY KEY AUTOINCREMENT, symbol TEXT, name TEXT, description TEXT, n_sequence TEXT)""")
#creation of pathways table
c.execute("""CREATE TABLE pathways (id INT, name TEXT, description TEXT)""")
#creation of enzymes table
c.execute("""CREATE TABLE enzymes (id INT, name TEXT)""")
#creation of association table between genes and enzymes
c.execute("""CREATE TABLE genes_and_enzymes (gene_id INT, enzyme_id INT)""")
#creation of association table between enzymes and pathways
c.execute("""CREATE TABLE enzymes_in_pathways (enzyme_id INT, pathway_id INT)""")



#commitment for new tables
conn.commit()

#next 3 lines are inserting rows into pathways and their description
c.execute("""INSERT INTO pathways (id, name, description) VALUES (1, "glycolysis", "the catalysis of glucose");""")

c.execute("""INSERT INTO pathways (id, name, description) VALUES (2, "TCA", "cyclic pathway");""")

c.execute("""INSERT INTO pathways (id, name, description) VALUES (3, "PPP", "generates NAD(P)H and pentose sugars");""")

#committing pathways insert
conn.commit()
#inserting enzymes into table
enzymes_list = [ (1, "hexokinase"), 
                (2, "phosphoglucose isomerase"),
                (3, "Aldolase"), 
                (4, "pyruvate kinase"), 
                (5, "citrate synthase"), 
                (6, "malate dehydrogenase"), 
                (7, "isocitrate dehydrogenase"), 
                (8, "fumurase"), 
                (9, "transketolase"), 
                (10, "transaldolase"), 
                (11, "gluconolactonase"), 
                (12, "glucose-6-phosphate dehydrogenase")]
for x in enzymes_list:
    c.execute("""INSERT INTO enzymes (id, name) VALUES (?, ?);""", x)
    conn.commit()

c.execute("SELECT * FROM pathways WHERE name = 'glycolysis';")

#printing the fetched row to ensure its presence
print(c.fetchone())

#importing our Bio import
from Bio import Entrez
from Bio import SeqIO
import time
Entrez.email = 'xxxxx@xxx.xx' #Letting NCBI know who I am
coli_enzymes = ["hexokinase", 
                "phosphoglucose isomerase",
                "Aldolase", 
                "pyruvate kinase", 
                "citrate synthase", 
                "malate dehydrogenase", 
                "isocitrate dehydrogenase", 
                "fumurase", 
                "transketolase", 
                "transaldolase", 
                "gluconolactonase", 
                "glucose-6-phosphate dehydrogenase"]

for enzyme in coli_enzymes:
    handle = Entrez.esearch(db = 'nuccore', 
                            term='E. coli [ORGN] ' +enzyme, 
                            sort='relevance', 
                            idtype='symbol')
    time.sleep(3)

for i in Entrez.read(handle)['IdList']:
    handle = Entrez.efetch(db = 'nuccore', id=i, rettype='gb', retmode='text', retmax=1)
    record_coli = SeqIO.read(handle, "genbank")
    seq_coli = record.seq
    c.execute("""INSERT INTO genes (symbol, name, description, n_sequence) VALUES (?, ?, ?, ?);""", 
                (str(i), 
                str(enzyme), 
                str(record_coli.description), 
                str(seq)))
    conn.commit()
    time.sleep(3)



human_enzymes = ["hexokinase", 
                "phosphoglucose isomerase",
                "Aldolase", 
                "pyruvate kinase", 
                "citrate synthase", 
                "malate dehydrogenase", 
                "isocitrate dehydrogenase", 
                "fumurase", 
                "transketolase", 
                "transaldolase", 
                "gluconolactonase", 
                "glucose-6-phosphate dehydrogenase"]

for enz in human_enzymes:
    handle = Entrez.esearch(db = 'nuccore', 
                            term='homo sapiens [ORGN] ' +enz, 
                            sort='relevance', 
                            idtype='symbol')
    time.sleep(3)
    print(['IdList'])

for d in Entrez.read(handle)['IdList']:
    handle = Entrez.efetch(db = 'nuccore', id=d, rettype='gb', retmode='text', retmax=1)
    record_human = SeqIO.read(handle, "genbank")
    seq_human = record.seq
    c.execute("""INSERT INTO genes (symbol, name, description, n_sequence) VALUES (?, ?, ?, ?);""", 
                (str(d), 
                str(enz), 
                str(record_human.description), 
                str(seq_human)))
    conn.commit()
    time.sleep(3)

drosophila_enzymes = ["hexokinase", 
                "phosphoglucose isomerase",
                "Aldolase", 
                "pyruvate kinase", 
                "citrate synthase", 
                "malate dehydrogenase", 
                "isocitrate dehydrogenase", 
                "fumurase", 
                "transketolase", 
                "transaldolase", 
                "gluconolactonase", 
                "glucose-6-phosphate dehydrogenase"]

for y in drosophila_enzymes:
    handle = Entrez.esearch(db = 'nuccore', 
                            term='drosophila melanogaster [ORGN] ' +y, 
                            sort='relevance', 
                            idtype='symbol')
    time.sleep(3)

for z in Entrez.read(handle)['IdList']:
    handle = Entrez.efetch(db = 'nuccore', id=z, rettype='gb', retmode='text', retmax=1)
    record_fly = SeqIO.read(handle, "genbank")
    seq_fly = record.seq
    c.execute("""INSERT INTO genes (symbol, name, description, n_sequence) VALUES (?, ?, ?, ?);""", 
                (str(d), 
                str(y), 
                str(record_fly.description), 
                str(seq_fly)))
    conn.commit()
    time.sleep(3)
SQLite3 Entrez Biopython • 416 views
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2
Entering edit mode
2.1 years ago
for enzyme in coli_enzymes:
    handle = Entrez.esearch(db = 'nuccore', 
                            term='E. coli [ORGN] ' +enzyme, 
                            sort='relevance', 
                            idtype='symbol')
    time.sleep(3)

for i in Entrez.read(handle)['IdList']:
    handle = Entrez.efetch(db = 'nuccore', id=i, rettype='gb', retmode='text', retmax=1)
    record_coli = SeqIO.read(handle, "genbank")
    seq_coli = record.seq
    c.execute("""INSERT INTO genes (symbol, name, description, n_sequence) VALUES (?, ?, ?, ?);""", 
                (str(i), 
                str(enzyme), 
                str(record_coli.description), 
                str(seq)))
    conn.commit()
    time.sleep(3)

You are first iterate over coli_enzymes and overwrite the value of handle each time. After finishing the loop you continue with the code. I think the next loop must be within the first loop and not outside. Same problem appears several times in your code.

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