def run(self):
'It runs the analysis.'
output_dir = self._create_output_dirs()['result']
inputs = self._get_input_fpaths()
pickle_paths = inputs['pickle']
for seq_path in pickle_paths:
output_fpath = join(output_dir, seq_path.basename + '.txt')
seqs = seqs_in_file(open(seq_path.last_version, 'r'))
do_annotation_statistics(seqs, open(output_fpath, 'w'))
def test_annotation_statistics():
'It tests the seq annotation statistics'
orf = SeqFeature(FeatureLocation(1, 3), type='orf',
qualifiers={'strand':'reverse'})
intron = SeqFeature(FeatureLocation(2, 2), type='intron')
ssr1 = SeqFeature(FeatureLocation(2, 2), type='microsatellite',
qualifiers={'unit':'GAA'})
ssr2 = SeqFeature(FeatureLocation(7, 10), type='microsatellite',
qualifiers={'unit':'GAA'})
snv = SeqFeature(FeatureLocation(7, 7), type='snv',
qualifiers={'alleles':{('T',0):'', ('G',0):''}})
snv2 = SeqFeature(FeatureLocation(7, 7), type='snv',
qualifiers={'alleles':{('T',0):'', ('R',0):''}})
feats1 = [intron, ssr1]
feats2 = [orf, ssr2, snv, snv2]
annots1 = {'arabidopsis-orthologs':['arab_1']}
annots2 = {'melon-orthologs':['melon_1'],
'arabidopsis-orthologs':['arab_2'],
'GOs':['Go1', 'Go2']}
seq1 = SeqWithQuality(Seq('ACTG'), description='hola', features=feats1,
annotations=annots1)
seq2 = SeqWithQuality(Seq('ACTG'), features=feats2, annotations=annots2)
seqs = [seq1, seq2]
stats_fhand = StringIO()
do_annotation_statistics(seqs, stats_fhand)
result = stats_fhand.getvalue()
expected = '''Annotation statistics
---------------------
Number of sequences: 2
Sequences with description: 1
Sequences with ORF: 1
Number of ORFs: 1
Sequences with intron: 1
Number of introns: 1
Orthologs
_________
Sequences with melon orthologs: 1
Number of melon orthologs: 1
Sequences with arabidopsis orthologs: 2
Number of arabidopsis orthologs: 2
GO terms
________
Sequences with GOs: 1
Number of GOs: 2
SNVs
____
Sequences with SNVs: 1
SNVs found: 2
SNV types:
\ttransversion: 1
\tunknown: 1
SNV locations:
\tunknown: 2
Microsatellites
_______________
Sequences with microsatellites: 2
| dinucleotide| trinucleotide|tetranucleotide|pentanucleotide| hexanucleotide| Total|
--------------------------------------------------------------------------------------------------
utr3| 0| 0| 0| 0| 0| 0|
utr5| 0| 1| 0| 0| 0| 1|
orf| 0| 0| 0| 0| 0| 0|
unknown| 0| 1| 0| 0| 0| 1|
--------------------------------------------------------------------------------------------------
total| 0| 2| 0| 0| 0| |
'''
result = result.splitlines()
expected = expected.splitlines()
for index, line in enumerate(result):
assert line == expected[index]
