def cdsExt(ID, geneName):
"""
returns sequence record object for the input gene refseq ID
"""
retdata = Entrez.efetch(db="nucleotide",
id=ID,
rettype='gb',
retmode='text').read()
with open("Align/" + geneName.split('.')[0] + ".log", "a") as fp:
if 'LOW QUALITY PROTEIN' in retdata:
fp.write('%s CDS is of low quality\n' % ID)
data = retdata.split('\n')
for obj in data:
if ' CDS ' in obj:
try:
cdsRange = [
int(obj.lstrip(' CDS ').split('..')[0]),
int(obj.lstrip(' CDS ').split('..')[1])
]
except ValueError:
try:
cdsRange = [
int(
obj.lstrip(' CDS ').split('..')[0].
lstrip('<').lstrip('>').rstrip('<').rstrip('>')),
int(
obj.lstrip(' CDS ').split('..')[1].
lstrip('<').lstrip('>').rstrip('<').rstrip('>'))
]
except ValueError:
try:
cdsRange = [
int(
obj.lstrip(' CDS ').split('..')
[0]),
int(
obj.lstrip(' CDS ').split('..')
[1].lstrip('>'))
]
except ValueError:
print(
"Problem found while extracting cds from %s. Please report this issue to ambuj (at) ufl (dot) edu"
% obj)
continue
recData = Entrez.efetch(db="nucleotide",
id=ID,
rettype="gb",
warning=False)
record = SeqIO.read(recData, 'genbank')
record.seq = record.seq[cdsRange[0] - 1:cdsRange[1]]
return record
def discont():
"""Creates a list of discontinued IDs from NCBI gene database"""
Entrez.email = '*****@*****.**'
distTerm = "all[filter] NOT alive[prop]"
handle = Entrez.esearch(db="gene",
term=distTerm,
rettype='xml',
RetMax=10000000,
warning=False)
records = Entrez.read(handle)
idListDiscont = records['IdList']
return idListDiscont
def fetchall(spName, discontId):
"""
@ spName - Species name
@ discontId - list of IDs that are discontinued in NCBI gene database
@ returns - list of all gene names present in the corresponding species
"""
inpTerm = spName + "[orgn]"
Entrez.email = '*****@*****.**'
try:
handle = Entrez.esearch(db="gene",
term=inpTerm,
rettype='xml',
RetMax=1000000)
except:
raise RuntimeError(
"Failed to import sequence from NCBI. Check your internet connection.\nThis might also occur due to NCBI failure"
)
records = Entrez.read(handle)
idList = records['IdList']
if is_empty(idList) == True:
print("No gene record available for %s" % spName)
return None
print("Filtering discontinued gene IDs in %s" % spName)
goodIds = [i for i in idList if i not in discontId]
idNameList = list()
for idName in goodIds:
try:
annot = Entrez.efetch(db='gene',
id=idName,
retmode='text',
rettype='brief').read()
print("Scanning %s %s gene" % (spName, annot.split(" ")[1]))
idNameList.append(annot.split(" ")[1])
except:
print("%s skipped" % idName)
idNameList.append(idName + " skipped")
continue
idNameList = set([x for x in idNameList if " skipped" not in x])
with open("Output/" + spName + "_genes.txt", 'w') as fp:
for gene in idNameList:
fp.write("%s\n" % gene)
return idNameList
def mrnaExt(ID):
"""Extract sequence record for the given sequence ID"""
recData = Entrez.efetch(db="nucleotide",
id=ID,
rettype="gb",
warning=False)
record = SeqIO.read(recData, 'genbank')
return record
def _fetch_Species(inpTerm=None):
"""Extracts species ID from NCBI genome database"""
if inpTerm == None:
inpTerm = "Eucaryotes[orgn] NOT Vertebrates[orgn]"
try:
handle = Entrez.esearch(db="genome",
term=inpTerm,
rettype='xml',
RetMax=10000)
except:
raise RuntimeError(
"Failed to import sequence from NCBI. Check your internet connection.\nThis might also occur due to NCBI failure"
)
records = Entrez.read(handle)
idList = records['IdList']
return idList
def oneGeneCdsImport(geneName, group):
"""
@ geneName - name of the gene
@ group - organism name
@ returns - the longest CDS sequence for the corresponding taxa
"""
inpTerm = geneName + "[sym] AND " + group + "[orgn]"
Entrez.email = '*****@*****.**'
print("Importing %s %s gene CDS sequence" % (group, geneName))
try:
handle = Entrez.esearch(db="gene",
term=inpTerm,
rettype='xml',
RetMax=300)
except:
raise RuntimeError(
"Failed to import sequence from NCBI. Check your internet connection.\nThis might also occur due to NCBI failure"
)
records = Entrez.read(handle)
ids = records["IdList"][0]
_xmlcreate(ids)
refIds = _xmlparser()
os.remove('export.xml')
recordList = list()
for inIDs in refIds:
recordList.append(cdsExt(inIDs, geneName))
longestRec = recordList[0]
for rec in recordList:
longestRec = rec if len(rec.seq) > len(longestRec.seq) else longestRec
longestRec.id = geneName
return longestRec
def mrnaImport(geneName, group, ortho):
"""
@ geneName - name of the gene
@ group - organism name
@ creates a taxon mRNA aligned fasta file as output for the set of genes given as input
"""
if ortho != None:
inpTerm = ortho + "[sym] AND " + group + "[orgn]"
elif group != None:
inpTerm = geneName + "[sym] AND " + group + "[orgn]"
Entrez.email = '*****@*****.**'
try:
handle = Entrez.esearch(db="gene",
term=inpTerm,
rettype='xml',
RetMax=300)
except:
raise RuntimeError(
"Failed to import sequence from NCBI. Check your internet connection.\nThis might also occur due to NCBI failure"
)
records = Entrez.read(handle)
idList = records["IdList"]
inpTerm = "ortholog_gene_" + str(idList[0]) + "[group]"
handle = Entrez.esearch(db="gene",
term=inpTerm,
rettype='xml',
RetMax=300,
warning=False)
records = Entrez.read(handle)
idList = records["IdList"]
outRecord = list()
for ids in idList:
_xmlcreate(ids)
refIds = _xmlparser()
os.remove('export.xml')
recordList = list()
for inIDs in refIds:
recordList.append(mrnaExt(inIDs))
try:
longestRec = recordList[0]
except:
continue
for rec in recordList:
longestRec = rec if len(rec.seq) > len(
longestRec.seq) else longestRec
print("%s" % longestRec.description)
outRecord.append(longestRec)
with open("Align/" + geneName + '.fas', 'w') as fp:
SeqIO.write(outRecord, fp, 'fasta')
fdata = open("Align/" + geneName + '.fas', 'r').readlines()
with open("Align/" + geneName + '.fas', 'w') as fp:
for lines in fdata:
if '>' in lines and 'PREDICTED' in lines:
newLine = '>' + lines.split(' ')[2] + '_' + lines.split(
' ')[3] + '|' + lines.split(' ')[0].lstrip('>')
fp.write('%s\n' % newLine)
elif '>' in lines and 'PREDICTED' not in lines:
newLine = '>' + lines.split(' ')[1] + '_' + lines.split(
' ')[2] + '|' + lines.split(' ')[0].lstrip('>')
fp.write('%s\n' % newLine)
else:
fp.write('%s' % lines)