def contain_A(read, n=2):
'''test if contain A in fastq read found in bam line
:return: true/false
'''
seq = Seq(read.query_sequence)
if read.flag & 16:
# reverse
seq = seq.reverse_complement()
else:
# forward alignment
pass
if seq.endswith("A"*n):
return True
else:
return False
def genbankOutput(resultGbFile,
resultFile,
listOfFeaturesToOutput,
buildCloroplast=False,
dLoopSize=800,
nWalk=20):
'''
Creates a genbank file based on a fasta file given (resultfile) and a list of features that the genbank
file should present (listoffeaturestooutput)
'''
#creating the genbank file, not annotated, to be opened afterwards and have the features inserted
with open(resultGbFile, "w") as outputResult:
finalResults = SeqIO.read(open(resultFile, 'rU'), "fasta", generic_dna)
finalResults.seq = finalResults.seq.upper()
finalResults.name = finalResults.name[0:10] + '_draft'
finalResults.id = finalResults.name[0:10] + '_draft'
if len(
finalResults.name
) > 16: #has to 16 characters long at max, or else genbank file throws error
finalResults.name = finalResults.name[0:16]
finalResults.id = finalResults.id[0:16]
count = SeqIO.write(finalResults, outputResult, "genbank")
dico_intron = {}
for thisFeatureAlignment in listOfFeaturesToOutput:
if not ('trn' in thisFeatureAlignment.seq2.lower() or 'rrn' in thisFeatureAlignment.seq2.lower() \
or 'ribosomal' in thisFeatureAlignment.seq2.lower() or 'rnr' in thisFeatureAlignment.seq2.lower()):
if dico_intron.has_key(thisFeatureAlignment.seq2.split("_")[0]):
dico_intron[thisFeatureAlignment.seq2.split("_")[0]] += 1
else:
dico_intron[thisFeatureAlignment.seq2.split("_")[0]] = 1
dico_gene = {}
with open(
resultGbFile, "rU"
) as outputResult: #opening the output file, this time to insert the features
finalResults = SeqIO.read(outputResult, "genbank", generic_dna)
#lastFeatureAlignment = None
dLoopFound = False
for thisFeatureAlignment in listOfFeaturesToOutput:
# 1. Define a feature type as a text string
main_feature_qualifiers = {
} #create qualifiers dict where the name will be stored
if 'trn' in thisFeatureAlignment.seq2.lower() or 'rrn' in thisFeatureAlignment.seq2.lower() \
or 'ribosomal' in thisFeatureAlignment.seq2.lower() or 'rnr' in thisFeatureAlignment.seq2.lower():
main_feature_qualifiers['product'] = thisFeatureAlignment.seq2
if 'trn' in thisFeatureAlignment.seq2.lower():
main_feature_type = "tRNA"
else:
main_feature_type = "rRNA"
else:
main_feature_qualifiers['gene'] = thisFeatureAlignment.seq2
main_feature_type = "gene"
gene = thisFeatureAlignment.seq2.split("_")[0]
if dico_gene.has_key(gene):
dico_gene[gene] += 1
else:
dico_gene[gene] = 1
main_start_pos = SeqFeature.ExactPosition(
thisFeatureAlignment.startBase)
main_end_pos = SeqFeature.ExactPosition(
thisFeatureAlignment.endBase)
if main_feature_type == "gene":
codonDiff = ((main_end_pos - main_start_pos + 1) % 3)
if codonDiff == 2:
main_end_pos += 1
elif codonDiff == 1:
main_end_pos -= 1
#print main_start_pos
#print main_end_pos
#print thisFeatureAlignment.frame
# 2. Use the locations do define a FeatureLocation
if thisFeatureAlignment.frame < 0:
strandToOutput = -1
else:
strandToOutput = 1
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1, main_end_pos, strand=strandToOutput)
# 3. Create a SeqFeature
main_feature = SeqFeature.SeqFeature(
main_feature_location,
type=main_feature_type,
qualifiers=main_feature_qualifiers)
'''
#find d-loop part
#basically just look for a big gap between last feature and this current feature, if there is a gap that
#is about the size of a d-loop, it most likely is a dloop, since nothing aligned with it and it has that size
#ignore this check if a cloroplast was built
if lastFeatureAlignment != None and dLoopFound == False and buildCloroplast == False and dLoopSize > 0:
if thisFeatureAlignment.startBase > lastFeatureAlignment.endBase + dLoopSize \
and thisFeatureAlignment.startBase < lastFeatureAlignment.endBase + 3200:
dLoopFound = True
dLoopStartPos = SeqFeature.ExactPosition(lastFeatureAlignment.endBase)
dLoopEndPos = SeqFeature.ExactPosition(thisFeatureAlignment.startBase)
dLoopLocation = SeqFeature.FeatureLocation(dLoopStartPos,dLoopEndPos,strand=-1)
dLoopType = "D-loop"
dLoopFeature = SeqFeature.SeqFeature(dLoopLocation,type=dLoopType)
finalResults.features.append(dLoopFeature)
lastFeatureAlignment = thisFeatureAlignment
'''
# 4. Append your newly created SeqFeature to your SeqRecord
if main_feature_type == "gene":
cds_qualifiers = dict(main_feature_qualifiers)
coding_dna = Seq(
str(finalResults.seq[thisFeatureAlignment.startBase -
1:thisFeatureAlignment.endBase]),
IUPAC.unambiguous_dna)
if strandToOutput == -1:
coding_dna = coding_dna.reverse_complement()
translationTable = thisFeatureAlignment.translationTable
tableToUse = CodonTable.unambiguous_dna_by_id[translationTable]
listOfStartCodons = []
listOfStopCodons = []
for startCodon in tableToUse.start_codons:
"""startCodonSeq = Seq(startCodon, IUPAC.unambiguous_dna)
startCodonTranslation = str(startCodonSeq.translate(table=translationTable))
if startCodonTranslation not in listOfStartCodons:
listOfStartCodons.append(startCodonTranslation)"""
if startCodon not in listOfStartCodons:
listOfStartCodons.append(startCodon)
startCodons = tuple(
listOfStartCodons
) #need to make it a tuple so that startswith works with it
for stopCodon in tableToUse.stop_codons:
if stopCodon not in listOfStopCodons:
listOfStopCodons.append(stopCodon)
stopCodons = tuple(listOfStopCodons)
nWalkStart = int(nWalk)
nWalkStop = int(nWalk)
'''
For genes in the -1 strand, we look for the stop codons at the start and the start codons at the end!
'''
""" if strandToOutput == -1:
tempStartCodons = startCodons
tempStopCodons = stopCodons
startCodons = tempStopCodons
stopCodons = tempStartCodons
nWalkStart = nWalk
nWalkStop = nWalk """
try:
'''
Making sure it starts with startCodons
'''
try:
coding_dna_Forward = coding_dna
coding_dna_Backward = coding_dna
startBase = int(thisFeatureAlignment.startBase)
endBase = int(thisFeatureAlignment.endBase)
n = 0
if strandToOutput == 1:
while not coding_dna_Forward.startswith(startCodons) \
and not coding_dna_Backward.startswith(startCodons) \
and not coding_dna_Backward.startswith(stopCodons) \
and dico_gene.get(gene) == 1 and n < nWalkStart and startBase - (3*(n+1)) >= 0:
try:
n += 1
coding_dna_Backward = Seq(
str(finalResults.seq[startBase - 1 -
(3 * n):endBase]),
IUPAC.unambiguous_dna)
coding_dna_Forward = Seq(
str(finalResults.seq[startBase - 1 -
(3 * n):endBase]),
IUPAC.unambiguous_dna)
'''print str(strandToOutput)
print "looking for start ="+str(startCodons)
print "coding_dna_Forward"
print coding_dna_Forward
print coding_dna_Forward.startswith(startCodons)
print "coding_dna_Backward"
print coding_dna_Backward
print coding_dna_Backward.startswith(startCodons)'''
except:
pass
else:
if coding_dna_Forward.startswith(startCodons):
main_start_pos = SeqFeature.ExactPosition(
startBase - (3 * n))
thisFeatureAlignment.startBase = main_start_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Backward.startswith(
startCodons):
main_start_pos = SeqFeature.ExactPosition(
startBase - (3 * n))
thisFeatureAlignment.startBase = main_start_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Backward.startswith(
stopCodons
): # we look for a start inside the hit
n = 0
while not coding_dna_Forward.startswith(
startCodons
) and n < nWalkStart and startBase + (
3 * (n + 1)) <= endBase:
try:
n += 1
coding_dna_Forward = Seq(
str(finalResults.
seq[startBase - 1 +
(3 * n):endBase]),
IUPAC.unambiguous_dna)
except:
pass
else:
if coding_dna_Forward.startswith(
startCodons):
main_start_pos = SeqFeature.ExactPosition(
startBase + (3 * n))
thisFeatureAlignment.startBase = main_start_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
if strandToOutput == -1:
while not coding_dna_Forward.endswith(stopCodons) \
and not coding_dna_Backward.endswith(stopCodons) \
and dico_gene.get(gene) == 1 and n < nWalkStart and startBase - (3*(n+1)) >= 0 and startBase + (3*(n+1)) <= endBase:
try:
n += 1
coding_dna_Backward = Seq(
str(finalResults.seq[startBase - 1 -
(3 * n):endBase]),
IUPAC.unambiguous_dna)
coding_dna_Backward = coding_dna_Backward.reverse_complement(
)
coding_dna_Forward = Seq(
str(finalResults.seq[startBase - 1 +
(3 * n):endBase]),
IUPAC.unambiguous_dna)
coding_dna_Forward = coding_dna_Forward.reverse_complement(
)
'''print str(strandToOutput)
print "looking for stop ="+str(stopCodons)
print "coding_dna_Forward"
print coding_dna_Forward
print coding_dna_Forward.endswith(stopCodons)
print "coding_dna_Backward"
print coding_dna_Backward
print coding_dna_Backward.endswith(stopCodons)'''
except:
pass
else:
if coding_dna_Forward.endswith(stopCodons):
main_start_pos = SeqFeature.ExactPosition(
startBase + (3 * n))
thisFeatureAlignment.startBase = main_start_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Backward.endswith(stopCodons):
main_start_pos = SeqFeature.ExactPosition(
startBase - (3 * n))
thisFeatureAlignment.startBase = main_start_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
except:
pass
'''
Updating coding_dna with (new) coordinates
'''
coding_dna = Seq(
str(finalResults.seq[thisFeatureAlignment.startBase -
1:thisFeatureAlignment.endBase]),
IUPAC.unambiguous_dna)
if strandToOutput == -1:
coding_dna = coding_dna.reverse_complement()
'''
Making sure it ends with * (stop codon)
'''
try:
coding_dna_Forward = coding_dna
coding_dna_Backward = coding_dna
startBase = int(thisFeatureAlignment.startBase)
endBase = int(thisFeatureAlignment.endBase)
n = 0
if strandToOutput == 1:
while not coding_dna_Forward.endswith(stopCodons) \
and not coding_dna_Backward.endswith(stopCodons) \
and dico_gene.get(gene) == dico_intron.get(gene) and n < nWalkStop and endBase + (3*(n+1)) <= len(finalResults):
try:
n += 1
coding_dna_Backward = Seq(
str(finalResults.seq[startBase -
1:endBase -
(3 * n)]),
IUPAC.unambiguous_dna)
coding_dna_Forward = Seq(
str(finalResults.seq[startBase -
1:endBase +
(3 * n)]),
IUPAC.unambiguous_dna)
'''print str(strandToOutput)
print "looking for stop ="+str(stopCodons)
print "coding_dna_Forward"
print coding_dna_Forward
print coding_dna_Forward.endswith(stopCodons)
print "coding_dna_Backward"
print coding_dna_Backward
print coding_dna_Backward.endswith(stopCodons)'''
except:
pass
else:
if coding_dna_Backward.endswith(stopCodons):
main_end_pos = SeqFeature.ExactPosition(
endBase - (3 * n))
thisFeatureAlignment.endBase = main_end_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Forward.endswith(stopCodons):
main_end_pos = SeqFeature.ExactPosition(
endBase + (3 * n))
thisFeatureAlignment.endBase = main_end_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
if strandToOutput == -1:
while not coding_dna_Forward.startswith(startCodons) \
and not coding_dna_Backward.startswith(startCodons) \
and not coding_dna_Forward.startswith(stopCodons) \
and dico_gene.get(gene) == dico_intron.get(gene) and n < nWalkStop and endBase + (3*(n+1)) <= len(finalResults):
try:
n += 1
coding_dna_Backward = Seq(
str(finalResults.seq[startBase -
1:endBase +
(3 * n)]),
IUPAC.unambiguous_dna)
coding_dna_Backward = coding_dna_Backward.reverse_complement(
)
coding_dna_Forward = Seq(
str(finalResults.seq[startBase -
1:endBase +
(3 * n)]),
IUPAC.unambiguous_dna)
coding_dna_Forward = coding_dna_Forward.reverse_complement(
)
'''print str(strandToOutput)
print "looking for start ="+str(startCodons)
print "coding_dna_Forward"
print coding_dna_Forward
print coding_dna_Forward.startswith(startCodons)
print "coding_dna_Backward"
print coding_dna_Backward
print coding_dna_Backward.startswith(startCodons)'''
except:
pass
else:
if coding_dna_Backward.startswith(startCodons):
main_end_pos = SeqFeature.ExactPosition(
endBase + (3 * n))
thisFeatureAlignment.endBase = main_end_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Forward.startswith(
startCodons):
main_end_pos = SeqFeature.ExactPosition(
endBase + (3 * n))
thisFeatureAlignment.endBase = main_end_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
elif coding_dna_Forward.startswith(
stopCodons
): # we look for a start inside the hit
n = 0
while not coding_dna_Forward.startswith(
startCodons
) and n < nWalkStop and endBase - (
3 * (n + 1)) >= startBase:
try:
n += 1
coding_dna_Forward = Seq(
str(finalResults.
seq[startBase - 1:endBase -
(3 * n)]),
IUPAC.unambiguous_dna)
coding_dna_Forward = coding_dna_Forward.reverse_complement(
)
except:
pass
else:
if coding_dna_Forward.startswith(
startCodons):
main_end_pos = SeqFeature.ExactPosition(
endBase - (3 * n))
thisFeatureAlignment.endBase = main_end_pos
main_feature_location = SeqFeature.FeatureLocation(
main_start_pos - 1,
main_end_pos,
strand=strandToOutput)
except:
pass
coding_dna = Seq(
str(finalResults.seq[thisFeatureAlignment.startBase -
1:thisFeatureAlignment.endBase]),
IUPAC.unambiguous_dna)
'''print "\n\nFINAL SEQUENCE IS:"
if strandToOutput == 1:
print coding_dna+"\n"
else:
print coding_dna.reverse_complement()+"\n"'''
if strandToOutput == 1:
coding_dna_Translation = coding_dna.translate(
table=translationTable)
else:
coding_dna_Translation = coding_dna.reverse_complement(
).translate(table=translationTable)
cds_qualifiers['translation'] = coding_dna_Translation
except:
cds_qualifiers['translation'] = 'ERROR'
cds_feature = SeqFeature.SeqFeature(main_feature_location,
type='CDS',
qualifiers=cds_qualifiers)
main_feature = SeqFeature.SeqFeature(
main_feature_location,
type=main_feature_type,
qualifiers=main_feature_qualifiers)
finalResults.features.append(main_feature)
finalResults.features.append(cds_feature)
else: #if it's a tRNA or rRNA
gene_feature = SeqFeature.SeqFeature(
main_feature_location,
type='gene',
qualifiers=main_feature_qualifiers)
finalResults.features.append(gene_feature)
finalResults.features.append(main_feature)
#returns the final SeqRecord object, with all features, so that the script that called genbankOutput can output this result whatever way
#it wants
return finalResults
