In [1]:

    

def search(seq, threshold=1):
    url="http://api.bigsiseq.com/search?threshold=%f&seq=%s" % (float(threshold),seq)
    results = requests.get(url).json()
    samples = []
    for i,j in list(results.values())[0]["results"].items():
        samples.append(i)
    return samples


    

In [2]:

    

import requests


    

In [3]:

    

seq="CGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACC"


    

In [4]:

    

samples = search(seq)


    

In [5]:

    

print(samples)


    

    




['ERR1681620', 'ERR1163291', 'ERR1609376', 'ERR1623360', 'ERR1622314', 'ERR1656135', 'ERR1609380', 'ERR1622709', 'ERR1623341', 'ERR1163331', 'ERR1622651', 'ERR1623390', 'ERR1366473', 'SRR2053338', 'ERR1622310', 'ERR1759157', 'ERR197184', 'ERR956997', 'ERR1623239', 'ERR1681650', 'SRR1645608', 'ERR1623521', 'SRR5184275', 'SRR2767734', 'ERR1623227', 'ERR1759167', 'ERR1622655', 'ERR1623229', 'ERR1759128', 'ERR1681717', 'ERR1656450', 'ERR1623113', 'ERR715581', 'SRR3745275', 'ERR1622312', 'ERR1759166', 'ERR1622305', 'ERR1622034', 'SRR1788031', 'ERR1622541', 'ERR1407280', 'ERR1623222', 'SRR2053340', 'SRR1788026', 'ERR1681704', 'SRR1967426', 'SRR1958396', 'SRR1788027', 'ERR1681654', 'ERR1623579', 'SRR5129179', 'ERR1681785', 'ERR1622079', 'ERR1623230', 'ERR1609434', 'ERR1623215', 'ERR1407279', 'ERR1623237', 'ERR1623346', 'ERR1407278', 'ERR1622547', 'ERR1360255', 'ERR1609449', 'ERR1623228', 'ERR1622435', 'ERR1623394', 'SRR3322633', 'ERR1622708', 'ERR135710', 'SRR1957973', 'ERR1622928', 'ERR1681839', 'ERR1681783', 'ERR1623457', 'ERR1622654', 'ERR1609312', 'ERR1622881', 'ERR1609378', 'SRR3584989', 'ERR1622946', 'ERR1759207', 'ERR1623525', 'ERR1622370', 'ERR1229301', 'ERR1046133', 'ERR1622670', 'ERR1609197', 'ERR1622309', 'SRR3882972', 'SRR1788028', 'SRR3707448', 'ERR1622739', 'ERR1229297', 'ERR1609196', 'SRR4302136', 'SRR1788024', 'ERR1623088', 'ERR1623225', 'ERR1622311', 'SRR2075991', 'ERR1149371', 'ERR1218581', 'ERR1622769', 'SRR1960364', 'ERR1622930', 'ERR1229302', 'SRR5201504', 'ERR1622883', 'ERR702345', 'ERR1218720', 'ERR1623226', 'SRR1965341', 'SRR3168915', 'ERR1623212', 'ERR1623214', 'SRR4302224', 'ERR1623594', 'SRR3407159', 'SRR1788032', 'ERR1622648', 'ERR1609215', 'SRR1814872', 'SRR3170531', 'SRR2054237', 'ERR1432660', 'ERR1609201', 'ERR1622653', 'SRR3452849', 'SRR2010693', 'ERR1432659', 'ERR1622107', 'ERR1609245', 'SRR4302302', 'ERR1622060', 'ERR1681606', 'ERR1622545', 'ERR1622729', 'SRR4302214', 'SRR2015698', 'ERR1622839', 'ERR1035693', 'ERR135713', 'ERR1623241', 'ERR1609249', 'ERR1218643', 'SRR4289227', 'ERR1622589', 'ERR1544012', 'ERR1623223', 'ERR1562562', 'ERR1622058', 'ERR1681602', 'ERR1623444', 'ERR1622987', 'ERR1622770', 'ERR1623342', 'ERR1360256', 'SRR3170679', 'ERR1681601', 'ERR1622725', 'ERR1623523', 'ERR1681781', 'SRR2054248', 'ERR1229300', 'ERR1622840', 'SRR1969022', 'ERR1359224', 'ERR1681854', 'ERR1623279']

In [9]:

    

from Bio import Entrez
import time
Entrez.email ="phelimb@well.ox.ac.uk"


    

In [16]:

    

## Search for a GI from genbank
## e.g. https://www.ncbi.nlm.nih.gov/nuccore/1150750917

GI="1150750917"

request = Entrez.epost("nucleotide",id=GI)
result = Entrez.read(request)
webEnv = result["WebEnv"]
queryKey = result["QueryKey"]
handle = Entrez.efetch(db="nucleotide",retmode="xml", webenv=webEnv, query_key=queryKey)
for r in Entrez.parse(handle):
    print (search(r.get("GBSeq_sequence").upper()))


    

    




['ERR1681620', 'ERR1163291', 'ERR1609376', 'ERR1623360', 'ERR1622314', 'ERR1656135', 'ERR1609380', 'ERR1622709', 'ERR1623341', 'ERR1163331', 'ERR1622651', 'ERR1623390', 'ERR1366473', 'SRR2053338', 'ERR1622310', 'ERR1759157', 'ERR197184', 'ERR956997', 'ERR1623239', 'ERR1681650', 'SRR1645608', 'ERR1623521', 'SRR5184275', 'SRR2767734', 'ERR1623227', 'ERR1759167', 'ERR1622655', 'ERR1623229', 'ERR1759128', 'ERR1681717', 'ERR1656450', 'ERR1623113', 'ERR715581', 'SRR3745275', 'ERR1622312', 'ERR1759166', 'ERR1622305', 'ERR1622034', 'SRR1788031', 'ERR1622541', 'ERR1407280', 'ERR1623222', 'SRR2053340', 'SRR1788026', 'ERR1681704', 'SRR1967426', 'SRR1958396', 'SRR1788027', 'ERR1681654', 'ERR1623579', 'SRR5129179', 'ERR1681785', 'ERR1622079', 'ERR1623230', 'ERR1609434', 'ERR1623215', 'ERR1407279', 'ERR1623237', 'ERR1623346', 'ERR1407278', 'ERR1622547', 'ERR1360255', 'ERR1609449', 'ERR1623228', 'ERR1622435', 'ERR1623394', 'SRR3322633', 'ERR1622708', 'ERR135710', 'SRR1957973', 'ERR1622928', 'ERR1681839', 'ERR1681783', 'ERR1623457', 'ERR1622654', 'ERR1609312', 'ERR1622881', 'ERR1609378', 'SRR3584989', 'ERR1622946', 'ERR1759207', 'ERR1623525', 'ERR1622370', 'ERR1229301', 'ERR1046133', 'ERR1622670', 'ERR1609197', 'ERR1622309', 'SRR3882972', 'SRR1788028', 'SRR3707448', 'ERR1622739', 'ERR1229297', 'ERR1609196', 'SRR4302136', 'SRR1788024', 'ERR1623088', 'ERR1623225', 'ERR1622311', 'SRR2075991', 'ERR1149371', 'ERR1218581', 'ERR1622769', 'SRR1960364', 'ERR1622930', 'ERR1229302', 'SRR5201504', 'ERR1622883', 'ERR702345', 'ERR1218720', 'ERR1623226', 'SRR1965341', 'SRR3168915', 'ERR1623212', 'ERR1623214', 'SRR4302224', 'ERR1623594', 'SRR3407159', 'SRR1788032', 'ERR1622648', 'ERR1609215', 'SRR1814872', 'SRR3170531', 'SRR2054237', 'ERR1432660', 'ERR1609201', 'ERR1622653', 'SRR3452849', 'SRR2010693', 'ERR1432659', 'ERR1622107', 'ERR1609245', 'SRR4302302', 'ERR1622060', 'ERR1681606', 'ERR1622545', 'ERR1622729', 'SRR4302214', 'SRR2015698', 'ERR1622839', 'ERR1035693', 'ERR135713', 'ERR1623241', 'ERR1609249', 'ERR1218643', 'SRR4289227', 'ERR1622589', 'ERR1544012', 'ERR1623223', 'ERR1562562', 'ERR1622058', 'ERR1681602', 'ERR1623444', 'ERR1622987', 'ERR1622770', 'ERR1623342', 'ERR1360256', 'SRR3170679', 'ERR1681601', 'ERR1622725', 'ERR1623523', 'ERR1681781', 'SRR2054248', 'ERR1229300', 'ERR1622840', 'SRR1969022', 'ERR1359224', 'ERR1681854', 'ERR1623279']

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