def get_sequence_from_location(species, coords):
"""Get sequence from a genomic location in an ensembl species genome."""
from cogent.db.ensembl import HostAccount, Genome, Compara, Species
genome = Genome(Species=species, Release='87', account=None)
chrom, start, end, strand = coords
#print coords
r = genome.getRegion(CoordName=str(chrom),
Start=start,
End=end,
Strand=strand)
return r.Seq
def ensembl_to_hgnc(gene_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
hgnc_list = []
for gene in gene_list:
hgnc_list.append(human.getGeneByStableId(StableId=gene).Symbol)
hgnc_list = set(hgnc_list)
return hgnc_list
def get_genes_from_location(ref, coords, pad=0):
"""Get genes from a set of genome coordinates.
pad will add n bases to either side to expand area"""
genome = Genome(Species=ref, Release=release, account=account)
chrom, start, end, strand = coords
genes = list(
genome.getFeatures(CoordName=chrom,
Start=start - pad,
End=end + pad,
feature_types='gene'))
return genes
def ensembl_to_hgnc(gene_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
hgnc_list = []
for gene in gene_list:
hgnc_list.append(human.getGeneByStableId(StableId=gene).Symbol)
hgnc_list = set(hgnc_list)
return hgnc_list
def get_chrom_seqs(species, release, account=None, debug=False):
"""yields sequence objects for the indicated chromosomes from Ensembl"""
genome = Genome(species, Release=release, account=account)
for chrom in chroms[species]:
region = genome.getRegion(CoordName=chrom)
seq = region.Seq
name = 'chr_%s' % chrom
seq.Name = name
if debug:
print name
print repr(seq)
yield seq
def Main():
global args,out
args=ParseArg()
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
count={}
dbi1=DBI.init(args.db,"bed") # the DBI init file for bed6 file of all kinds of RNA
dbi2=DBI.init(args.db_detail,"bed") # the DBI init file for bed12 file of lincRNA and mRNA with intron, exon, UTR
genome=Genome('mouse', Release=67, account=None)
for bed in TableIO.parse(args.input,args.format):
[typ,name,subtype]=annotation(bed,dbi1,dbi2,genome)
if count.has_key(typ):
count[typ]+=1
else:
count[typ]=1
print >>out, "\t".join (str(f) for f in [bed.chr,bed.start,bed.stop,bed.id,name,bed.strand,typ, subtype])
print >>out, "\n".join ("#"+typ+"\t%d"%(count[typ]) for typ in count.keys())
def hgnc_to_ensembl_id(hgnc_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
ensembl_stable_id_list = []
for gene in hgnc_list:
gene_query = human.getGenesMatching(Symbol=gene)
for gene_obj in gene_query:
if gene_obj.Symbol == gene:
ensembl_stable_id_list.append(gene_obj.StableId)
#Remove duplicates
ensembl_stable_id_list = set(ensembl_stable_id_list)
#Keep list elements starting with 'ENSG'
ensembl_stable_id_list = [x for x in ensembl_stable_id_list if x.startswith('ENSG')]
return ensembl_stable_id_list
def get_genes_from_Ensembl_multiple(args, sourcedata, targetdata):
inputtype = args.inputType
if (inputtype == "id"):
geneidlistfile = args.geneIdListFile
if (geneidlistfile == None):
print "Argument -gidlf <geneidlistfilename> is required"
else:
for line in open(geneidlistfile, "r").readlines():
parse = line.split("\n")[0].split(" ")
if (len(parse) > 1):
species = parse[0]
geneid = parse[1]
print "Retreving Gene", geneid
account = HostAccount('ensembldb.ensembl.org', 'anonymous',
'')
genome = Genome(species, ENSEMBL_VERSION, account)
gene = genome.getGeneByStableId(StableId=geneid)
sourcedata += get_cds_data(gene)
targetdata += get_gene_data(gene)
if (inputtype == "name"):
gene = args.gene
if (gene == None):
print "Argument -g <genename> is required"
specieslistfile = args.specieslistfile
if (specieslistfile == None):
print "Argument -slf <specieslistfilename> is required"
if (gene != None and specieslistfile != None):
for line in open(specieslistfile, "r").readlines():
parse = line.split("\n")[0].split(" ")
if (len(parse) > 0):
species = parse[0]
print "Retreving Gene", gene, "from species", species
account = HostAccount('ensembldb.ensembl.org', 'anonymous',
'')
genome = Genome(species, ENSEMBL_VERSION, account)
gene = get_gene_from_Ensembl_by_name(gene, genome)
sourcedata += get_cds_data(gene)
targetdata += get_gene_data(gene)
return sourcedata, targetdata
def hgnc_to_ensembl_id(hgnc_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
ensembl_stable_id_list = []
for gene in hgnc_list:
gene_query = human.getGenesMatching(Symbol=gene)
for gene_obj in gene_query:
if gene_obj.Symbol == gene:
ensembl_stable_id_list.append(gene_obj.StableId)
#Remove duplicates
ensembl_stable_id_list = set(ensembl_stable_id_list)
#Keep list elements starting with 'ENSG'
ensembl_stable_id_list = [
x for x in ensembl_stable_id_list if x.startswith('ENSG')
]
return ensembl_stable_id_list
def main():
import os
script_dir = os.path.dirname(os.path.abspath(__file__))
""" Neccesary to log into the ensembl database """
import os
from cogent.db.ensembl import HostAccount
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
""" gathers the transcript id and protein sequence from gene """
sp = "zebrafish"
gn = "ENSDARG00000027279"
from cogent.db.ensembl import Genome
specie = Genome(Species=sp, Release="81", account=None)
gene = specie.getGeneByStableId(StableId=gn)
for tr in gene.Transcripts:
print(tr.StableId)
for ex in tr.Exons:
print(ex.Symbol)
def get_genes_from_Ensembl_pairwise(args, sourcedata, targetdata):
genelist = []
inputtype = args.inputType
firstspecies = args.firstspecies
secondspecies = args.secondspecies
if (firstspecies == None):
print "Argument -s1 <firstspeciesname> is required"
elif (secondspecies == None):
print "Argument -s2 <secondspeciesname> is required"
else:
account = HostAccount('ensembldb.ensembl.org', 'anonymous', '')
firstgenome = Genome(firstspecies, ENSEMBL_VERSION, account)
secondgenome = Genome(secondspecies, ENSEMBL_VERSION, account)
if (inputtype == "id"):
firstgeneid = args.firstgeneid
if (firstgeneid == None):
print "Argument -gid1 <firstgeneid> is required"
secondgeneid = args.secondgeneid
if (secondgeneid == None):
print "Argument -gid2 <secondgeneid> is required"
if (firstgeneid != None and secondgeneid != None):
print "Retreving Genes", firstgeneid, secondgeneid
firstgene = firstgenome.getGeneByStableId(StableId=firstgeneid)
secondgene = secondgenome.getGeneByStableId(
StableId=secondgeneid)
if (inputtype == "name"):
gene = args.gene
if (gene == None):
print "Argument -g <genename> is required"
else:
print "Retreving Genes", name, "from species", firstspecies, secondspecies
firstgene = get_gene_from_Ensembl_by_name(gene, firstgenome)
secondgene = get_gene_from_Ensembl_by_name(gene, secondgenome)
sourcedata += get_cds_data(firstgene) + get_cds_data(secondgene)
targetdata += get_gene_data(firstgene) + get_gene_data(secondgene)
return sourcedata, targetdata
# Code to merge ensembl gene information with annotation of probes and junctions to get an idea of the gene structure
import pandas as pd
import re
from collections import Counter
from itertools import permutations
import csv
import string
from cogent.db.ensembl import Genome, HostAccount
from difflib import SequenceMatcher
#account = HostAccount('ensembldb.ensembl.org', 'anonymous', '', port=5306)
account = HostAccount('127.0.0.1', 'root', 'ensembl', port=3306)
Release = 89
HumanDB = Genome(Species='human', Release=Release, account=account)
class SettingTCID_GeneIDError(Exception):
def __init__(self, msg):
self.msg = msg
def __str__(self):
return self.msg
def GeneStructure(TCID,
GeneID,
Probesets=None,
MappingFile="HTA_2_0_Probeset_SequenceIndices.txt",
SequenceFile="HTA_2_0_Probeset_Sequences.txt",
location="Output",
genome and reverse complement if on the negative strand. The sequence currently
in the reference file may refer to the sequence synthesized on the chip, in which
case it is the version with the lowest A's (easier to synthesize). It could also
be the sequence without strand consideration. To be sure, let's just pull from
the genome.
'''
import MySQLdb
# use cogent to extract sequences from the genome
from cogent.db.ensembl import HostAccount, Genome
import pandas as pd
# set up connection
# host, user, password, port
pycog = HostAccount('ensembldb.ensembl.org', 'anonymous', '', 3306)
hs37 = Genome('human', Release=78, account=pycog)
# read in reference
data = pd.read_table('../produced_data/splicemod_data_clean.txt', sep='\t')
# reformat so intron/exon length columns are int and not float, convert NA to 0 so we can use int
data[['intron1_len', 'exon_len',
'intron2_len']] = data[['intron1_len', 'exon_len',
'intron2_len']].fillna(0.0).astype(int)
# grab sequences with chr, start and end information
lib = data[data.chr.notnull() & data.start.notnull() & data.end.notnull()]
def grab_region(chr, start, end, strand, genome):
start = int(start)
Release=80 from cogent.db.ensembl import Species, Genome human = Genome(Species='human', Release=Release, account=None) gene = human.getGeneByStableId(StableId='ENSG00000205274') print gene.Symbol
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
protein_mutation = 'A203T'
protein_A = protein_mutation[0]
protein_B = protein_mutation[-1]
codon_index = int(protein_mutation[1:-1])
#result = find_codon_index(protein_A, 'GCA', protein_B)
#print result
human = Genome(Species='human', Release=Release, account=account)
print human
#seqs = {'original' : 'A',
#'mutation' : 'T'
#}
#protein = LoadSeqs(data = seqs, moltype = PROTEIN)
#print protein.getTranslation()
#protein = 'METSASATASEKQEAKSGILEAAGFPDPGKKASPLVVAAAAAAAVAAQGVPQHLLPPFHAPLPIDMRHQEGRYHYEPHSVHGVHGPPALSGSPVISDISLIRLSPHPAGPGESPFNAPHPYVNPHMEHYLRSVHSSPTLSMISAARGLSPADVAQEHLKERGLFGLPAPGTTPSDYYHQMTLVAGHPAPYGDLLMQSGGAASAPHLHDYLNPVDVSRFSSPRVTPRLSRKRALSISPLSDASLDLQRMIRTSPNSLVAYINNSRSSSAASGSYGHLSAGALSPAFTFPHPINPVAYQQILSQQRGLGSAFGHTPPLIQPSPTFLAQQPMALTSINATPTQLSSSSNCLSDTNQNKQSSESAVSSTVNPVAIHKRSKVKTEPEGLRPASPLALTQGQVSGHGSCGCALPLSQEQLADLKEDLDRDDCKQEAEVVIYETNCHWEDCTKEYDTQEQLVHHINNEHIHGEKKEFVCRWQACTREQKPFKAQYMLVVHMRRHTGEKPHKCTFEGCSKAYSRLENLKTHLRSHTGEKPYVCEHEGCNKAFSNASDRAKHQNRTHSNEKPYICKIPGCTKRYTDPSSLRKHVKTVHGPDAHVTKKQRNDVHLRTPLLKENGDSEAGTEPGGPESTEASSTSQAVEDCLHVRAIKTESSGLCQSSPGAQSSCSSEPSPLGSAPNNDSGVEMPGTGPGSLGDLTALDDTPPGADTSALAAPSAGGLQLRKHMTTMHRFEQLKKEKLKSLKDSCSWAGPTPHTRNTKLPPLPGSGSILENFSGSGGGGPAGLLPNPRLSELSASEVTMLSQLQERRDSSTSTVSSAYTVSRRSSGISPYFSSRRSSEASPLGAGRPHNASSADSYDPISTDASRRSSEASQCSGGSGLLNLTPAQQYSLRAKYAAATGGPPPTPLPGLERMSLRTRLALLDAPERTLPAGCPRPLGPRRGSDGPTYGHGHAGAAPAFPHEAPGGGARRASDPVRRPDALSLPRVQRFHSTHNVNPGPLPPCADRRGLRLQSHPSTDGGLARGAYSPRPPSISENVAMEAVAAGVDGAGPEADLGLPEDDLVLPDDVVQYIKAHASGALDEGTGQVYPTESTGFSDNPRLPSPGLHGQRRMVAADSNVGPSAPMLGGCQLGFGAPSSLNKNNMPVQWNEVSSGTVDALASQVKPPPFPQGNLAVVQQKPAFGQYPGYSPQGLQASPGGLDSTQPHLQPRSGAPSQGIPRVNYMQQLRQPVAGSQCPGMTTTMSPHACYGQVHPQLSPSTISGALNQFPQSCSNMPAKPGHLGHPQQTEVAPDPTTMGNRHRELGVPDSALAGVPPPHPVQSYPQQSHHLAASMSQEGYHQVPSLLPARQPGFMEPQTGPMGVATAGFGLVQPRPPLEPSPTGRHRGVRAVQQQLAYARATGHAMAAMPSSQETAEAVPKGAMGNMGSVPPQPPPQDAGGAPDHSMLYYYGQIHMYEQDGGLENLGSCQVMRSQPPQPQACQDSIQPQPLPSPGVNQVSSTVDSQLLEAPQIDFDAIMDDGDHSSLFSGALSPSLLHSLSQNSSRLTTPRNSLTLPSIPAGISNMAVGDMSSMLTSLAEESKFLNMMT'
#print len(protein)
#cds = 'ATGGAGACGTCTGCCTCAGCCACTGCCTCCGAGAAGCAAGAAGCCAAAAGTGGGATCCTGGAGGCCGCTGGCTTCCCCGACCCGGGTAAAAAGGCCTCTCCTTTGGTGGTGGCTGCAGCGGCAGCAGCAGCGGTAGCTGCCCAAGGAGTGCCGCAGCATCTCTTGCCACCATTCCATGCGCCCCTACCGATTGACATGCGACACCAGGAAGGAAGGTACCATTACGAGCCTCATTCTGTCCACGGTGTGCACGGGCCCCCTGCCCTCAGCGGCAGCCCTGTCATCTCTGACATCTCCTTGATCCGGCTTTCCCCGCACCCGGCTGGCCCTGGGGAGTCCCCCTTCAACGCCCCCCACCCGTACGTGAACCCCCACATGGAGCACTACCTCCGTTCTGTGCACAGCAGCCCCACGCTCTCCATGATCTCTGCAGCCAGGGGCCTCAGCCCCGCTGATGTGGCCCAGGAGCACCTTAAGGAGAGGGGACTGTTTGGCCTTCCTGCTCCAGGCACCACCCCCTCAGACTATTACCACCAGATGACCCTCGTGGCAGGCCACCCCGCGCCCTACGGGGACCTGCTGATGCAGAGCGGGGGCGCTGCCAGCGCACCCCATCTCCACGACTACCTCAACCCCGTGGACGTGTCCCGTTTCTCCAGCCCGCGGGTGACGCCCCGCCTGAGCCGCAAGCGGGCGCTGTCCATCTCCCCACTCTCAGACGCCAGCCTGGACCTGCAGCGGATGATCCGCACCTCACCCAACTCGCTAGTGGCCTACATCAACAACTCCCGAAGCAGCTCGGCGGCCAGCGGTTCCTACGGGCATCTGTCAGCGGGTGCCCTCAGCCCAGCCTTCACCTTCCCCCACCCCATCAACCCCGTGGCCTACCAGCAGATTCTGAGCCAGCAGAGGGGTCTGGGGTCAGCCTTTGGACACACACCACCCCTGATCCAGCCCTCACCCACCTTCCTGGCCCAGCAGCCCATGGCCCTCACCTCCATCAATGCCACGCCCACCCAGCTCAGCAGCAGCAGCAACTGTCTGAGTGACACCAACCAGAACAAGCAGAGCAGTGAGTCGGCCGTCAGCAGCACCGTCAACCCTGTCGCCATTCACAAGCGCAGCAAGGTCAAGACCGAGCCTGAGGGCCTGCGGCCGGCCTCCCCTCTGGCGCTGACGCAGGGCCAGGTGTCTGGACACGGCTCATGTGGGTGTGCCCTTCCCCTCTCCCAGGAGCAGCTGGCTGACCTCAAGGAAGATCTGGACAGGGATGACTGTAAGCAGGAGGCTGAGGTGGTCATCTATGAGACCAACTGCCACTGGGAAGACTGCACCAAGGAGTACGACACCCAGGAGCAGCTGGTGCATCACATCAACAACGAGCACATCCACGGGGAGAAGAAGGAGTTTGTGTGCCGCTGGCAGGCCTGCACGCGGGAGCAGAAGCCCTTCAAGGCGCAGTACATGCTGGTGGTGCACATGCGGCGACACACGGGCGAGAAGCCCCACAAGTGCACGTTCGAGGGCTGCTCGAAGGCCTACTCCCGCCTGGAGAACCTGAAGACACACCTGCGGTCCCACACCGGGGAGAAGCCATATGTGTGTGAGCACGAGGGCTGCAACAAAGCCTTCTCCAACGCCTCGGACCGCGCCAAGCACCAGAATCGCACCCACTCCAACGAGAAACCCTACATCTGCAAGATCCCAGGCTGCACCAAGAGATACACAGACCCCAGCTCTCTCCGGAAGCATGTGAAAACGGTCCACGGCCCAGATGCCCACGTCACCAAGAAGCAGCGCAATGACGTGCACCTCCGCACACCGCTGCTCAAAGAGAATGGGGACAGTGAGGCCGGCACGGAGCCTGGCGGCCCAGAGAGCACCGAGGCCAGCAGCACCAGCCAGGCCGTGGAGGACTGCCTGCACGTCAGAGCCATCAAGACCGAGAGCTCCGGGCTGTGTCAGTCCAGCCCCGGGGCCCAGTCGTCCTGCAGCAGCGAGCCCTCTCCTCTGGGCAGTGCCCCCAACAATGACAGTGGCGTGGAGATGCCGGGGACGGGGCCCGGGAGCCTGGGAGACCTGACGGCACTGGATGACACACCCCCAGGGGCCGACACCTCAGCCCTGGCTGCCCCCTCCGCTGGTGGCCTCCAGCTGCGCAAACACATGACCACCATGCACCGGTTCGAGCAGCTCAAGAAGGAGAAGCTCAAGTCACTCAAGGATTCCTGCTCATGGGCCGGGCCGACTCCACACACGCGGAACACCAAGCTGCCTCCCCTCCCGGGAAGTGGCTCCATCCTGGAAAACTTCAGTGGCAGTGGGGGCGGCGGGCCCGCGGGGCTGCTGCCGAACCCGCGGCTGTCGGAGCTGTCCGCGAGCGAGGTGACCATGCTGAGCCAGCTGCAGGAGCGCCGCGACAGCTCCACCAGCACGGTCAGCTCGGCCTACACCGTGAGCCGCCGCTCCTCCGGCATCTCCCCCTACTTCTCCAGCCGCCGCTCCAGCGAGGCCTCGCCCCTGGGCGCCGGCCGCCCGCACAACGCGAGCTCCGCTGACTCCTACGACCCCATCTCCACGGACGCGTCGCGGCGCTCGAGCGAGGCCAGCCAGTGCAGCGGCGGCTCCGGGCTGCTCAACCTCACGCCGGCGCAGCAGTACAGCCTGCGGGCCAAGTACGCGGCAGCCACTGGCGGCCCCCCGCCCACTCCGCTGCCGGGCCTGGAGCGCATGAGCCTGCGGACCAGGCTGGCGCTGCTGGACGCGCCCGAGCGCACGCTGCCCGCCGGCTGCCCACGCCCACTGGGGCCGCGGCGTGGCAGCGACGGGCCGACCTATGGCCACGGCCACGCGGGGGCTGCGCCCGCCTTCCCCCACGAGGCTCCAGGCGGCGGAGCCAGGCGGGCCAGCGACCCTGTGCGGCGGCCCGATGCCCTGTCCCTGCCGCGGGTGCAGCGCTTCCACAGCACCCACAACGTGAACCCCGGCCCGCTGCCGCCCTGTGCCGACAGGCGAGGCCTCCGCCTGCAGAGCCACCCGAGCACCGACGGCGGCCTGGCCCGCGGCGCCTACTCGCCCCGGCCGCCTAGCATCAGCGAGAACGTGGCGATGGAGGCCGTGGCGGCAGGAGTGGACGGCGCGGGGCCCGAGGCCGACCTGGGGCTGCCGGAGGACGACCTGGTGCTTCCAGACGACGTGGTGCAGTACATCAAGGCGCACGCCAGTGGCGCTCTGGACGAGGGCACCGGGCAGGTGTATCCCACGGAAAGCACTGGCTTCTCTGACAACCCCAGACTACCCAGCCCGGGGCTGCACGGCCAGCGCAGGATGGTGGCTGCGGACTCCAACGTGGGCCCCTCCGCCCCTATGCTGGGAGGATGCCAGTTAGGCTTTGGGGCGCCCTCCAGCCTGAACAAAAATAACATGCCTGTGCAGTGGAATGAGGTGAGCTCCGGCACCGTAGACGCCCTGGCCAGCCAGGTGAAGCCTCCACCCTTTCCTCAGGGCAACCTGGCGGTGGTGCAGCAGAAGCCTGCCTTTGGCCAGTACCCGGGCTACAGTCCGCAAGGCCTACAGGCTAGCCCTGGGGGCCTGGACAGCACGCAGCCACACCTGCAGCCCCGCAGCGGAGCCCCCTCCCAGGGCATCCCCAGGGTAAACTACATGCAGCAGCTGCGACAGCCAGTGGCAGGCAGCCAGTGTCCTGGCATGACTACCACTATGAGCCCCCATGCCTGCTATGGCCAAGTCCACCCCCAGCTGAGCCCCAGCACCATCAGTGGGGCCCTCAACCAGTTCCCCCAATCCTGCAGCAACATGCCAGCCAAGCCAGGGCATCTGGGGCACCCTCAGCAGACAGAAGTGGCACCTGACCCCACCACGATGGGCAATCGCCACAGGGAACTTGGGGTCCCCGATTCAGCCCTGGCTGGAGTGCCACCACCTCACCCAGTCCAGAGCTACCCACAGCAGAGCCATCACCTGGCAGCCTCCATGAGCCAGGAGGGCTACCACCAGGTCCCCAGCCTTCTGCCTGCCCGCCAGCCTGGCTTCATGGAGCCCCAAACAGGCCCGATGGGGGTGGCTACAGCAGGCTTTGGCCTAGTGCAGCCCCGGCCTCCCCTCGAGCCCAGCCCCACTGGCCGCCACCGTGGGGTACGTGCTGTGCAGCAGCAGCTGGCCTACGCCAGGGCCACAGGCCATGCCATGGCTGCCATGCCGTCCAGTCAGGAAACAGCAGAGGCTGTGCCCAAGGGAGCGATGGGCAACATGGGGTCGGTGCCTCCCCAGCCGCCTCCGCAGGACGCAGGTGGGGCCCCGGACCACAGCATGCTCTACTACTACGGCCAGATCCACATGTACGAACAGGATGGAGGCCTGGAGAACCTCGGGAGCTGCCAGGTCATGCGGTCCCAGCCACCACAGCCACAGGCCTGTCAGGACAGCATCCAGCCCCAGCCCTTGCCCTCACCAGGGGTCAACCAGGTGTCCAGCACTGTGGACTCCCAGCTCCTGGAGGCCCCCCAGATTGACTTCGATGCCATCATGGATGATGGCGATCACTCGAGTTTGTTCTCGGGTGCTCTGAGCCCCAGCCTCCTCCACAGCCTCTCCCAGAACTCCTCCCGCCTCACCACCCCCCGAAACTCCTTGACCCTGCCCTCCATCCCCGCAGGCATCAGCAACATGGCTGTCGGGGACATGAGCTCCATGCTCACCAGCCTCGCCGAGGAGAGCAAGTTCCTGAACATGATGACCTAG'
#my_seq = DNA.makeSequence(cds,'gli2')
#seq = my_seq.withoutTerminalStopCodon()
#pep = seq.getTranslation()
#print pep.toFasta()
hitsOrganisms[items[7]] = True
print "> Number of loaded hits: " + str(len(hits))
outfile.close()
print "> SPECIES <"
for key in hitsOrganisms:
print key
exit(1)
##### SET CONNECTION TO THE ENSEMBL DATABASE ##########################
Release = 67
account = None
yeast = Genome(Species='Neosartorya fischeris',
Release=Release,
account=account)
outfile = open("dataset_fungal_homologs_sequences.csv", "w")
print Species
##### GET SEQUENCES FROM ENSEMBL ######################################
i = 0
for hit in hits:
i += 1
print "i: " + str(i)
identifier = hit
print "\n***** ZPRACOVANI ZAZNAMU " + identifier + " *****"
# Selection of species
genes = yeast.getGenesMatching(StableId="CADNFIAP00000001")
def download_database_pycogent(species, release, database_name='ensembl', nucleotide=False) :
log = get_log()
#try :
import cogent
from cogent.db.ensembl import Species, Genome, Compara, HostAccount
from cogent.db.ensembl.database import Database
#except ImportError :
# log.fatal("pycogent import failed, exiting...")
# exit(1)
if cogent.version_info != (1,5,3) :
log.warning("only tested with pycogent version 1.5.3 (you are running %s)" % cogent.version)
release, db_name, db_details = get_missing_info(species, release, database_name)
account = HostAccount(
db_details['hostname'],
db_details['username'],
db_details['password'],
port=db_details['port'])
if Species.getSpeciesName(species) == 'None' : # this is not an error, it returns the string "None"
log.warning("%s not found in pycogent, attempting to add it manually" % species)
Species.amendSpecies(species.capitalize().replace('_', ' '), species)
genome = Genome(species, Release=release, account=account)
compara = Compara([species], Release=release, account=account)
# DON'T TRY THIS AT HOME!
#
# what happens is it searches for compara databases, but unfortunately finds more than one
# in this situation pycogent just connects to the first one, which is always compara_bacteria
# so one solution is to dig through all the compara objects internals to provide a connection
# to the correct database ... obviously not the best solution, but at 6 lines of code definitely
# the shortest ;-P
#
if db_name not in ('ensembl', 'bacteria') :
log.warning("accessing compara from pycogent with species outside of ensembl-main and ensembl-bacteria is problematic, attempting to patch...")
from cogent.db.ensembl.host import DbConnection
from cogent.db.ensembl.name import EnsemblDbName
import sqlalchemy
new_db_name = EnsemblDbName(compara.ComparaDb.db_name.Name.replace('bacteria', db_name))
compara.ComparaDb._db = DbConnection(account=account, db_name=new_db_name)
compara.ComparaDb._meta = sqlalchemy.MetaData(compara.ComparaDb._db)
# end of DON'T TRY THIS AT HOME!
genes = set()
families = []
stderr.write("\r[downloading %s] got %d sequences " % ("CDS" if nucleotide else "protein", len(genes)))
for gene in genome.getGenesMatching(BioType='protein_coding') :
stableid = gene.StableId
# ignore genes that have already been seen as members of other gene families
if stableid in genes :
continue
genes.add(stableid)
paralogs = compara.getRelatedGenes(StableId=stableid, Relationship='within_species_paralog')
current = []
if paralogs is None :
stderr.write("\r[downloading %s] got %d sequences " % ("CDS" if nucleotide else "protein", len(genes)))
current.append((stableid, str(gene.CanonicalTranscript.Cds) if nucleotide else str(gene.CanonicalTranscript.ProteinSeq)))
else :
for paralog in paralogs.Members :
paralogid = paralog.StableId
genes.add(paralogid)
stderr.write("\r[downloading %s] got %d sequences " % ("CDS" if nucleotide else "protein", len(genes)))
try :
current.append((paralogid, str(paralog.CanonicalTranscript.Cds) if nucleotide else str(paralog.CanonicalTranscript.ProteinSeq)))
except AttributeError :
log.fatal("pycogent did not find a canonical transcript for %s" % paralogid)
exit(1)
#print ','.join([ i for i,j in current ])
families.append(current)
stderr.write("\r[downloading %s] got %d sequences\n" % ("CDS" if nucleotide else "protein", len(genes)))
return families
'''
import sys
import csv
import os
from cogent.db.ensembl import HostAccount, Species, Genome
import sqlalchemy as sql
Release = 70
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
human = Genome(Species='human', Release=Release, account=account)
def Getexons(ENSG,start,end):
gene = human.getGeneByStableId(StableId = ENSG)
print gene.BioType
print len(gene.Transcripts)
#print dir(gene.Location)
#print "\t\t\tstart\t\tEnd"
#print "from csv\t\t",start,"\t",end
#print "from location\t",gene.Location.Start,"\t",gene.Location.End
#print "from ensembl\t",gene.Location.EnsemblStart,"\t", gene.Location.EnsemblEnd
Not_Found = True
for transcript in gene.Transcripts:
#print dir(transcript.Location)
#print start,end
#if int(start)-1 == transcript.Location.Start and int(end) == transcript.Location.End:
import os
Release = 93
from cogent.db.ensembl import HostAccount
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
from cogent.db.ensembl import HostAccount, Genome
human = Genome(Species='human', Release=Release, account=account)
variants = human.getVariation(Symbol='rs369202065')
for variant in variants:
print(variant)
# die()
['AlleleFreqs', 'Alleles', 'Ancestral', 'Effect', 'FlankingSeq', 'Location', 'MapWeight', 'NULL_VALUE', 'NumAlleles', 'PeptideAlleles', 'Seq', 'Somatic', 'Symbol', 'TranslationLocation', 'Type', 'Validation', 'Variants', '__class__', '__cmp__', '__delattr__', '__dict__', '__doc__', '__format__', '__getattribute__', '__hash__', '__init__', '__len__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_attr_ensembl_table_map', '_cached', '_get_allele_freqs', '_get_allele_table_record', '_get_alleles', '_get_ancestral', '_get_ancestral_data', '_get_cached_value', '_get_effect', '_get_flanking_seq', '_get_flanking_seq_data', '_get_flanking_seq_data_ge_70', '_get_flanking_seq_data_lt_70', '_get_location', '_get_location_record', '_get_map_weight', '_get_number_alleles', '_get_peptide_variation', '_get_seq_region_record', '_get_sequence', '_get_somatic', '_get_symbol', '_get_transcript_record', '_get_translation_location', '_get_validation', '_get_variants', '_get_variation_table_record', '_location_column_prefix', '_make_location', '_populate_cache_from_record', '_set_null_values', '_split_alleles', '_table_rows', 'allele_code_table', 'allele_table', 'db', 'featureData', 'genome', 'getAnnotatedSeq', 'getFeatures', 'transcript_variation_table', 'variation_feature_table', 'variation_table']
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
# cogent and sqlalchemy modules need to be installed:
# pip2 install cogent
# pip2 install sqlalchemy
from cogent.db.ensembl import HostAccount, Species, Genome
from pypath import mapping
Release = 78
account = HostAccount('ensembldb.ensembl.org', 'anonymous', '')
human = Genome(Species='human', Release=Release, account=account)
# UniProt, seq offset, residue, isoform
positions = [('P00533', 40, 'Q', 1), ('P60520', 30, 'P', 1)]
m = mapping.Mapper()
m.load_uniprot_mappings(['ensg'], bi=True)
positions_ens = []
for p in positions:
ensgs = m.map_name(p[0], 'uniprot', 'ensg')
for ensg in ensgs:
genes = human.getGenesMatching(StableId=ensg)
for gene in genes:
positions_ens.append(
tuple([ensg, gene.Location, gene.CanonicalTranscript.Exons] +
list(p)))
# another attempts with biopython --
def add_ensembl_gene_data(session,
species,
ensembl_release,
account=None,
debug=False):
"""add Ensembl genes and their transcripts to the db session"""
rr = RunRecord('add_ensembl_gene_data')
genome = Genome(species, Release=ensembl_release, account=account)
skip = set(['processed_transcript', 'pseudogene'])
biotypes = [b for b in genome.getDistinct('BioType') if b not in skip]
data = []
unique_gene_ids = set()
unique_exon_ids = set()
chromSet = set()
n = 0
total_objects = 0
for biotype in biotypes:
for gene in genome.getGenesMatching(BioType=biotype):
# gene.Location.CoordName is the chromosome name
min_chrom_length = 5 # likely an unconfirmed scaffold
if len(gene.Location.CoordName) > min_chrom_length:
rr.addWarning('Skipping chrom', gene.Location.CoordName)
continue
chromSet.add(gene.Location.CoordName)
if gene.StableId not in unique_gene_ids:
db_gene = Gene(ensembl_id=gene.StableId,
symbol=gene.Symbol,
biotype=gene.BioType,
description=gene.Description,
status=gene.Status,
chrom=gene.Location.CoordName,
start=gene.Location.Start,
end=gene.Location.End,
strand=gene.Location.Strand)
unique_gene_ids.add(gene.StableId)
data.append(db_gene)
else:
rr.addWarning('Duplicate gene', gene.StableId)
for exon in gene.CanonicalTranscript.Exons:
if exon.StableId not in unique_exon_ids:
db_exon = Exon(exon.StableId, exon.Rank,
exon.Location.Start, exon.Location.End)
db_exon.gene = db_gene
unique_exon_ids.add(exon.StableId)
data.append(db_exon)
else:
rr.addWarning('Duplicate exon', exon.StableId)
n += 1
if n % 100 == 0:
print 'Genes processed:', n, '; Db objects created:', len(data)
if debug:
session.add_all(data)
session.commit()
return
rr.addInfo('Instantiating chromosomes', chromSet)
chroms = Chroms(species, chromSet)
data.append(chroms)
rr.addInfo('Writing objects into db', len(data))
session.add_all(data)
session.commit()
return chroms
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
protein_mutation = 'A203T'
protein_A = protein_mutation[0]
protein_B = protein_mutation[-1]
codon_index = int(protein_mutation[1:-1])
#result = find_codon_index(protein_A, 'GCA', protein_B)
#print result
human = Genome(Species='human', Release=Release, account=account)
print human
#seqs = {'original' : 'A',
#'mutation' : 'T'
#}
#protein = LoadSeqs(data = seqs, moltype = PROTEIN)
#print protein.getTranslation()
#protein = 'METSASATASEKQEAKSGILEAAGFPDPGKKASPLVVAAAAAAAVAAQGVPQHLLPPFHAPLPIDMRHQEGRYHYEPHSVHGVHGPPALSGSPVISDISLIRLSPHPAGPGESPFNAPHPYVNPHMEHYLRSVHSSPTLSMISAARGLSPADVAQEHLKERGLFGLPAPGTTPSDYYHQMTLVAGHPAPYGDLLMQSGGAASAPHLHDYLNPVDVSRFSSPRVTPRLSRKRALSISPLSDASLDLQRMIRTSPNSLVAYINNSRSSSAASGSYGHLSAGALSPAFTFPHPINPVAYQQILSQQRGLGSAFGHTPPLIQPSPTFLAQQPMALTSINATPTQLSSSSNCLSDTNQNKQSSESAVSSTVNPVAIHKRSKVKTEPEGLRPASPLALTQGQVSGHGSCGCALPLSQEQLADLKEDLDRDDCKQEAEVVIYETNCHWEDCTKEYDTQEQLVHHINNEHIHGEKKEFVCRWQACTREQKPFKAQYMLVVHMRRHTGEKPHKCTFEGCSKAYSRLENLKTHLRSHTGEKPYVCEHEGCNKAFSNASDRAKHQNRTHSNEKPYICKIPGCTKRYTDPSSLRKHVKTVHGPDAHVTKKQRNDVHLRTPLLKENGDSEAGTEPGGPESTEASSTSQAVEDCLHVRAIKTESSGLCQSSPGAQSSCSSEPSPLGSAPNNDSGVEMPGTGPGSLGDLTALDDTPPGADTSALAAPSAGGLQLRKHMTTMHRFEQLKKEKLKSLKDSCSWAGPTPHTRNTKLPPLPGSGSILENFSGSGGGGPAGLLPNPRLSELSASEVTMLSQLQERRDSSTSTVSSAYTVSRRSSGISPYFSSRRSSEASPLGAGRPHNASSADSYDPISTDASRRSSEASQCSGGSGLLNLTPAQQYSLRAKYAAATGGPPPTPLPGLERMSLRTRLALLDAPERTLPAGCPRPLGPRRGSDGPTYGHGHAGAAPAFPHEAPGGGARRASDPVRRPDALSLPRVQRFHSTHNVNPGPLPPCADRRGLRLQSHPSTDGGLARGAYSPRPPSISENVAMEAVAAGVDGAGPEADLGLPEDDLVLPDDVVQYIKAHASGALDEGTGQVYPTESTGFSDNPRLPSPGLHGQRRMVAADSNVGPSAPMLGGCQLGFGAPSSLNKNNMPVQWNEVSSGTVDALASQVKPPPFPQGNLAVVQQKPAFGQYPGYSPQGLQASPGGLDSTQPHLQPRSGAPSQGIPRVNYMQQLRQPVAGSQCPGMTTTMSPHACYGQVHPQLSPSTISGALNQFPQSCSNMPAKPGHLGHPQQTEVAPDPTTMGNRHRELGVPDSALAGVPPPHPVQSYPQQSHHLAASMSQEGYHQVPSLLPARQPGFMEPQTGPMGVATAGFGLVQPRPPLEPSPTGRHRGVRAVQQQLAYARATGHAMAAMPSSQETAEAVPKGAMGNMGSVPPQPPPQDAGGAPDHSMLYYYGQIHMYEQDGGLENLGSCQVMRSQPPQPQACQDSIQPQPLPSPGVNQVSSTVDSQLLEAPQIDFDAIMDDGDHSSLFSGALSPSLLHSLSQNSSRLTTPRNSLTLPSIPAGISNMAVGDMSSMLTSLAEESKFLNMMT'
#print len(protein)
#cds = 'ATGGAGACGTCTGCCTCAGCCACTGCCTCCGAGAAGCAAGAAGCCAAAAGTGGGATCCTGGAGGCCGCTGGCTTCCCCGACCCGGGTAAAAAGGCCTCTCCTTTGGTGGTGGCTGCAGCGGCAGCAGCAGCGGTAGCTGCCCAAGGAGTGCCGCAGCATCTCTTGCCACCATTCCATGCGCCCCTACCGATTGACATGCGACACCAGGAAGGAAGGTACCATTACGAGCCTCATTCTGTCCACGGTGTGCACGGGCCCCCTGCCCTCAGCGGCAGCCCTGTCATCTCTGACATCTCCTTGATCCGGCTTTCCCCGCACCCGGCTGGCCCTGGGGAGTCCCCCTTCAACGCCCCCCACCCGTACGTGAACCCCCACATGGAGCACTACCTCCGTTCTGTGCACAGCAGCCCCACGCTCTCCATGATCTCTGCAGCCAGGGGCCTCAGCCCCGCTGATGTGGCCCAGGAGCACCTTAAGGAGAGGGGACTGTTTGGCCTTCCTGCTCCAGGCACCACCCCCTCAGACTATTACCACCAGATGACCCTCGTGGCAGGCCACCCCGCGCCCTACGGGGACCTGCTGATGCAGAGCGGGGGCGCTGCCAGCGCACCCCATCTCCACGACTACCTCAACCCCGTGGACGTGTCCCGTTTCTCCAGCCCGCGGGTGACGCCCCGCCTGAGCCGCAAGCGGGCGCTGTCCATCTCCCCACTCTCAGACGCCAGCCTGGACCTGCAGCGGATGATCCGCACCTCACCCAACTCGCTAGTGGCCTACATCAACAACTCCCGAAGCAGCTCGGCGGCCAGCGGTTCCTACGGGCATCTGTCAGCGGGTGCCCTCAGCCCAGCCTTCACCTTCCCCCACCCCATCAACCCCGTGGCCTACCAGCAGATTCTGAGCCAGCAGAGGGGTCTGGGGTCAGCCTTTGGACACACACCACCCCTGATCCAGCCCTCACCCACCTTCCTGGCCCAGCAGCCCATGGCCCTCACCTCCATCAATGCCACGCCCACCCAGCTCAGCAGCAGCAGCAACTGTCTGAGTGACACCAACCAGAACAAGCAGAGCAGTGAGTCGGCCGTCAGCAGCACCGTCAACCCTGTCGCCATTCACAAGCGCAGCAAGGTCAAGACCGAGCCTGAGGGCCTGCGGCCGGCCTCCCCTCTGGCGCTGACGCAGGGCCAGGTGTCTGGACACGGCTCATGTGGGTGTGCCCTTCCCCTCTCCCAGGAGCAGCTGGCTGACCTCAAGGAAGATCTGGACAGGGATGACTGTAAGCAGGAGGCTGAGGTGGTCATCTATGAGACCAACTGCCACTGGGAAGACTGCACCAAGGAGTACGACACCCAGGAGCAGCTGGTGCATCACATCAACAACGAGCACATCCACGGGGAGAAGAAGGAGTTTGTGTGCCGCTGGCAGGCCTGCACGCGGGAGCAGAAGCCCTTCAAGGCGCAGTACATGCTGGTGGTGCACATGCGGCGACACACGGGCGAGAAGCCCCACAAGTGCACGTTCGAGGGCTGCTCGAAGGCCTACTCCCGCCTGGAGAACCTGAAGACACACCTGCGGTCCCACACCGGGGAGAAGCCATATGTGTGTGAGCACGAGGGCTGCAACAAAGCCTTCTCCAACGCCTCGGACCGCGCCAAGCACCAGAATCGCACCCACTCCAACGAGAAACCCTACATCTGCAAGATCCCAGGCTGCACCAAGAGATACACAGACCCCAGCTCTCTCCGGAAGCATGTGAAAACGGTCCACGGCCCAGATGCCCACGTCACCAAGAAGCAGCGCAATGACGTGCACCTCCGCACACCGCTGCTCAAAGAGAATGGGGACAGTGAGGCCGGCACGGAGCCTGGCGGCCCAGAGAGCACCGAGGCCAGCAGCACCAGCCAGGCCGTGGAGGACTGCCTGCACGTCAGAGCCATCAAGACCGAGAGCTCCGGGCTGTGTCAGTCCAGCCCCGGGGCCCAGTCGTCCTGCAGCAGCGAGCCCTCTCCTCTGGGCAGTGCCCCCAACAATGACAGTGGCGTGGAGATGCCGGGGACGGGGCCCGGGAGCCTGGGAGACCTGACGGCACTGGATGACACACCCCCAGGGGCCGACACCTCAGCCCTGGCTGCCCCCTCCGCTGGTGGCCTCCAGCTGCGCAAACACATGACCACCATGCACCGGTTCGAGCAGCTCAAGAAGGAGAAGCTCAAGTCACTCAAGGATTCCTGCTCATGGGCCGGGCCGACTCCACACACGCGGAACACCAAGCTGCCTCCCCTCCCGGGAAGTGGCTCCATCCTGGAAAACTTCAGTGGCAGTGGGGGCGGCGGGCCCGCGGGGCTGCTGCCGAACCCGCGGCTGTCGGAGCTGTCCGCGAGCGAGGTGACCATGCTGAGCCAGCTGCAGGAGCGCCGCGACAGCTCCACCAGCACGGTCAGCTCGGCCTACACCGTGAGCCGCCGCTCCTCCGGCATCTCCCCCTACTTCTCCAGCCGCCGCTCCAGCGAGGCCTCGCCCCTGGGCGCCGGCCGCCCGCACAACGCGAGCTCCGCTGACTCCTACGACCCCATCTCCACGGACGCGTCGCGGCGCTCGAGCGAGGCCAGCCAGTGCAGCGGCGGCTCCGGGCTGCTCAACCTCACGCCGGCGCAGCAGTACAGCCTGCGGGCCAAGTACGCGGCAGCCACTGGCGGCCCCCCGCCCACTCCGCTGCCGGGCCTGGAGCGCATGAGCCTGCGGACCAGGCTGGCGCTGCTGGACGCGCCCGAGCGCACGCTGCCCGCCGGCTGCCCACGCCCACTGGGGCCGCGGCGTGGCAGCGACGGGCCGACCTATGGCCACGGCCACGCGGGGGCTGCGCCCGCCTTCCCCCACGAGGCTCCAGGCGGCGGAGCCAGGCGGGCCAGCGACCCTGTGCGGCGGCCCGATGCCCTGTCCCTGCCGCGGGTGCAGCGCTTCCACAGCACCCACAACGTGAACCCCGGCCCGCTGCCGCCCTGTGCCGACAGGCGAGGCCTCCGCCTGCAGAGCCACCCGAGCACCGACGGCGGCCTGGCCCGCGGCGCCTACTCGCCCCGGCCGCCTAGCATCAGCGAGAACGTGGCGATGGAGGCCGTGGCGGCAGGAGTGGACGGCGCGGGGCCCGAGGCCGACCTGGGGCTGCCGGAGGACGACCTGGTGCTTCCAGACGACGTGGTGCAGTACATCAAGGCGCACGCCAGTGGCGCTCTGGACGAGGGCACCGGGCAGGTGTATCCCACGGAAAGCACTGGCTTCTCTGACAACCCCAGACTACCCAGCCCGGGGCTGCACGGCCAGCGCAGGATGGTGGCTGCGGACTCCAACGTGGGCCCCTCCGCCCCTATGCTGGGAGGATGCCAGTTAGGCTTTGGGGCGCCCTCCAGCCTGAACAAAAATAACATGCCTGTGCAGTGGAATGAGGTGAGCTCCGGCACCGTAGACGCCCTGGCCAGCCAGGTGAAGCCTCCACCCTTTCCTCAGGGCAACCTGGCGGTGGTGCAGCAGAAGCCTGCCTTTGGCCAGTACCCGGGCTACAGTCCGCAAGGCCTACAGGCTAGCCCTGGGGGCCTGGACAGCACGCAGCCACACCTGCAGCCCCGCAGCGGAGCCCCCTCCCAGGGCATCCCCAGGGTAAACTACATGCAGCAGCTGCGACAGCCAGTGGCAGGCAGCCAGTGTCCTGGCATGACTACCACTATGAGCCCCCATGCCTGCTATGGCCAAGTCCACCCCCAGCTGAGCCCCAGCACCATCAGTGGGGCCCTCAACCAGTTCCCCCAATCCTGCAGCAACATGCCAGCCAAGCCAGGGCATCTGGGGCACCCTCAGCAGACAGAAGTGGCACCTGACCCCACCACGATGGGCAATCGCCACAGGGAACTTGGGGTCCCCGATTCAGCCCTGGCTGGAGTGCCACCACCTCACCCAGTCCAGAGCTACCCACAGCAGAGCCATCACCTGGCAGCCTCCATGAGCCAGGAGGGCTACCACCAGGTCCCCAGCCTTCTGCCTGCCCGCCAGCCTGGCTTCATGGAGCCCCAAACAGGCCCGATGGGGGTGGCTACAGCAGGCTTTGGCCTAGTGCAGCCCCGGCCTCCCCTCGAGCCCAGCCCCACTGGCCGCCACCGTGGGGTACGTGCTGTGCAGCAGCAGCTGGCCTACGCCAGGGCCACAGGCCATGCCATGGCTGCCATGCCGTCCAGTCAGGAAACAGCAGAGGCTGTGCCCAAGGGAGCGATGGGCAACATGGGGTCGGTGCCTCCCCAGCCGCCTCCGCAGGACGCAGGTGGGGCCCCGGACCACAGCATGCTCTACTACTACGGCCAGATCCACATGTACGAACAGGATGGAGGCCTGGAGAACCTCGGGAGCTGCCAGGTCATGCGGTCCCAGCCACCACAGCCACAGGCCTGTCAGGACAGCATCCAGCCCCAGCCCTTGCCCTCACCAGGGGTCAACCAGGTGTCCAGCACTGTGGACTCCCAGCTCCTGGAGGCCCCCCAGATTGACTTCGATGCCATCATGGATGATGGCGATCACTCGAGTTTGTTCTCGGGTGCTCTGAGCCCCAGCCTCCTCCACAGCCTCTCCCAGAACTCCTCCCGCCTCACCACCCCCCGAAACTCCTTGACCCTGCCCTCCATCCCCGCAGGCATCAGCAACATGGCTGTCGGGGACATGAGCTCCATGCTCACCAGCCTCGCCGAGGAGAGCAAGTTCCTGAACATGATGACCTAG'
#my_seq = DNA.makeSequence(cds,'gli2')
#seq = my_seq.withoutTerminalStopCodon()
#pep = seq.getTranslation()
#print pep.toFasta()
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
print account
## What Species Are Available?
#from cogent.db.ensembl import Species
#print Species
## Interrogating a Genome
from cogent.db.ensembl import HostAccount, Genome
human = Genome(Species='human', Release=Release, account=account)
print human
'''
A Note on Coordinate Systems
The positions employed on Ensembls web-site, and in their MySQL database differ
from those used internally by cogent.db.ensembl.In all cases where you are querying
cogent.db.ensembl objects directly inputting nucleotide positions you can indicate
you are using Ensembl coordinates by setting ensembl_coord=True.
If you are explicitly passing in a cogent.db.ensembl region, that argument has no effect.
'''
## Selecting Gene
#Via StableID
brca1 = human.getGeneByStableId(StableId='ENSG00000012048')
except IndexError:
print "No gene entered"
gene=False
sys.exit()
print "<html>"
print "<head>"
print "<style>\ntab1 { padding-left: 4em; }\ntab2 { padding-left: 8em; }\n"
print "body{font-family:helvetica} \ntab3 { padding-left: 12em; }\n p{color:#AACCFF}\n"
print "button {padding: 15px 32px;text-align: center; text-decoration: none;display: inline-block;font-size: 16px;}\n li {margin-top: 0px; margin-right: 5px;}\n</style>"
print "</head>" ##AACCFF
print "<body style=\"background-color:#222233;\" text=\"#FFFFA8\">"
mouse=Genome(Species='mouse',Release=87,account=None)
#coding=mouse.getGenesMatching(StableID=geneID)
#print coding
coding=mouse.getGenesMatching(Symbol=genename)
#print mouse.getGenesMatching()
#print dir(mouse.getGenesMatching())
#print mouse.getGenesMatching().__dict__
#print coding
#sys.exit()
if not coding:
print "<p style=\"font-size: 55px;\">This is a fatal error. Can't find your gene<br>"
print "</body>"
sys.exit()
import os
from cogent.db.ensembl import HostAccount, Genome
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
human = Genome('human', Release=75, account=account)
gene_symbols = ['brca1', 'brca2']
genomes1k_url = 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502'
for gene_symbol in gene_symbols:
print gene_symbol
genes = human.getGenesMatching(Symbol=gene_symbol)
for gene in genes:
print gene.Location.CoordName
print gene.Location.Start, gene.Location.End
command = './breastcancer/programs/htslib/tabix -h \
%s/ALL.chr%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
%s:%s-%s > breastcancer/%s.vcf' % (
genomes1k_url, gene.Location.CoordName, gene.Location.CoordName,
gene.Location.Start, gene.Location.End, gene_symbol)
print command
#os.system(command)
size = gene.Location.End - gene.Location.Start
print 'Size', size
print gene.Location.Strand
import os
import sqlalchemy as sql
from cogent.db.ensembl import HostAccount, Genome
#account = HostAccount(*os.environ['ENSEMBL_ACCOUNT'].split())
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
human = Genome('human', Release=69, account=account)
# BRCA1
gene = human.getGeneByStableId(StableId="ENSG00000167131")
# get the db tables we need
external_db = human.CoreDb.getTable("external_db")
object_xref = human.CoreDb.getTable("object_xref")
xref = human.CoreDb.getTable("xref")
# get the external db ID for refseq mrna
refseq_mrna_id = sql.select([external_db.c.external_db_id],
external_db.c.db_name.like('RefSeq_mRNA')).execute().fetchone()
# query for a specific transcript ID
print "Querying for mRNA REFSEQ entries for one transcript"
query = sql.select([object_xref, xref],
sql.and_(xref.c.xref_id==object_xref.c.xref_id,
object_xref.c.ensembl_id == 1345831,
+ " Position: " + str(range.start) + "-" + str(range.end-1)\
+ " Length: " + str(range.end - range.start)
snp_count = seq.count("/")
if snp_count > 0:
header = header + " SNP count: " + str(snp_count)
else:
header = header + " no SNP"
output.write("\n" + header)
output.write("\n" + str(seq))
output.close
#Setting ensembl parameters
release = 81
species = 'Mus musculus'
mouse = Genome(Species=species, Release=release)
input = raw_input('\nEnter ensembl mouse transcript ID or txt file: ')
if input.strip().split('.')[-1] == 'txt':
try:
fh = open(input.strip(), 'r')
for transID in fh:
transID = transID.strip().split('.')[0]
print "\n" + "============ Start to manipulate", transID, "============"
gene, transcript, range_seqs = specific_region(transID)
if transcript is None: continue
seq_output(gene, transcript, range_seqs)
fh.close()
except IOError:
print "File", input, "not found!!"
