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Mbarba code review #2

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Mbarba code review #2

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9a240a8
Shorten method names
MatBarba Nov 13, 2020
a647c9c
Use list of codons, as class attributes
MatBarba Nov 13, 2020
88278af
Use with to open the fasta file
MatBarba Nov 13, 2020
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6 changes: 3 additions & 3 deletions module/gff_file.py
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Original file line number Diff line number Diff line change
Expand Up @@ -183,9 +183,9 @@ def scan_mrna_sequence(self, base_url=None, fasta_file=None):
else:
return False

mrna.coding_sequence_has_start_codon()
mrna.coding_sequence_has_stop_codon()
mrna.coding_sequence_no_internal_stop_codon()
mrna.has_start_codon()
mrna.has_stop_codon()
mrna.no_internal_stop_codon()

if mrna.errors != {}:
gene_id = self.get_gene_id(mrna_id)
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24 changes: 14 additions & 10 deletions module/transcript.py
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Expand Up @@ -16,6 +16,9 @@

class CodingSequence:
sequence_type = 'cds'

start_codons = ('ATG')
stop_codons = ('TAA', 'TAG', 'TGA')

def __init__(self, feature_name, organism_name, sequence_name):
self.feature_name = feature_name
Expand All @@ -37,33 +40,34 @@ def get_sequence(self, base_url=None, fasta_file=None):
else:
return False
elif fasta_file:
file_handle = open(fasta_file, 'r')
for seq in file_handle:
if seq[0] != '>':
self.sequence += seq.rstrip()
with open(fasta_file, 'r') as file_handle:
for seq in file_handle:
if seq[0] != '>':
self.sequence += seq.rstrip()
else:
return False

def coding_sequence_has_start_codon(self):
if self.sequence[0:3] == 'ATG':
def has_start_codon(self):
first_codon = self.sequence[0:3]
if first_codon in self.start_codons:
return True
else:
self.errors['start_codon'] = 'no start codon'
return False

def coding_sequence_has_stop_codon(self):
def has_stop_codon(self):
last_codon = self.sequence[-3:]
if last_codon == 'TAA' or last_codon == 'TAG' or last_codon == 'TGA':
if last_codon in self.stop_codons:
return True
else:
self.errors['stop_codon'] = 'no stop codon'
return False

def coding_sequence_no_internal_stop_codon(self):
def no_internal_stop_codon(self):
internal_stop_codon_count = 0
for i in range(0, len(self.sequence) - 3, 3):
codon = self.sequence[i:i + 3]
if codon == 'TAA' or codon == 'TAG' or codon == 'TGA':
if codon in self.stop_codons:
internal_stop_codon_count += 1
self.errors['no_internal_stop_codon'] = str(internal_stop_codon_count) + ' internal stop codon'
if internal_stop_codon_count:
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24 changes: 12 additions & 12 deletions test/test_transcript.py
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Expand Up @@ -12,46 +12,46 @@ def test_has_sequence(self):
def test_has_start_codon(self):
mrna = transcript.CodingSequence('b0b85443-0ff0-4fec-b919-f7bbeb626072', 'sandbox_arabiensis', 'SDBKB704125')
mrna.sequence = "ATGCACTGA"
mrna.coding_sequence_has_start_codon()
self.assertEqual(True, mrna.coding_sequence_has_start_codon())
mrna.has_start_codon()
self.assertEqual(True, mrna.has_start_codon())

mrna.sequence = "ATCCACTGA"
mrna.coding_sequence_has_start_codon()
mrna.has_start_codon()
self.assertEqual('no start codon', mrna.errors['start_codon'])

def test_has_stop_codon(self):
mrna = transcript.CodingSequence('b0b85443-0ff0-4fec-b919-f7bbeb626072', 'sandbox_arabiensis', 'SDBKB704125')

mrna.sequence = "ATGCACTGA" # TGA amber stop codon
self.assertEqual(True, mrna.coding_sequence_has_stop_codon())
self.assertEqual(True, mrna.has_stop_codon())

mrna.sequence = "ATGCAGTAA" # TAA ochre stop codon
self.assertEqual(mrna.coding_sequence_has_stop_codon(), True)
self.assertEqual(mrna.has_stop_codon(), True)

mrna.sequence = "ATGCAGTAG" # TAG opal stop codon
self.assertEqual(mrna.coding_sequence_has_stop_codon(), True)
self.assertEqual(mrna.has_stop_codon(), True)

mrna.sequence = "ATGCAGCAG" # NO stop codon
self.assertEqual(mrna.coding_sequence_has_stop_codon(), False)
self.assertEqual(mrna.has_stop_codon(), False)
self.assertEqual('no stop codon', mrna.errors['stop_codon'])

def test_no_internal_stop_codon(self):
mrna = transcript.CodingSequence('b0b85443-0ff0-4fec-b919-f7bbeb626072', 'sandbox_arabiensis', 'SDBKB704125')

mrna.sequence = "ATGCACCTCGAGTAA"
mrna.coding_sequence_no_internal_stop_codon()
self.assertEqual(mrna.coding_sequence_no_internal_stop_codon(), True)
mrna.no_internal_stop_codon()
self.assertEqual(mrna.no_internal_stop_codon(), True)

mrna.sequence = "ATGCACTAACTCGAGTAA" # TAA
mrna.coding_sequence_no_internal_stop_codon()
mrna.no_internal_stop_codon()
self.assertEqual(mrna.errors['no_internal_stop_codon'], '1 internal stop codon')

mrna.sequence = "ATGCACCTCGAGTAGTAA" # TAG
mrna.coding_sequence_no_internal_stop_codon()
mrna.no_internal_stop_codon()
self.assertEqual(mrna.errors['no_internal_stop_codon'], '1 internal stop codon')

mrna.sequence = "ATGTGACACCTCTAATAA" # TGA,TAA
mrna.coding_sequence_no_internal_stop_codon()
mrna.no_internal_stop_codon()
self.assertEqual(mrna.errors['no_internal_stop_codon'], '2 internal stop codon')


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