def test_pipeline_run():
'It tests that the pipeline runs ok'
pipeline = 'sanger_with_qual'
fhand_adaptors = NamedTemporaryFile()
fhand_adaptors.write(ADAPTORS)
fhand_adaptors.flush()
arabidopsis_genes = 'arabidopsis_genes+'
univec = os.path.join(TEST_DATA_DIR, 'blast', arabidopsis_genes)
configuration = {'remove_vectors_blastdb': {'vectors': univec},
'remove_adaptors': {'adaptors': fhand_adaptors.name}}
seq_fhand = open(os.path.join(TEST_DATA_DIR, 'seq.fasta'), 'r')
qual_fhand = open(os.path.join(TEST_DATA_DIR, 'qual.fasta'), 'r')
seq_iter = seqs_in_file(seq_fhand, qual_fhand)
filtered_seq_iter = _pipeline_builder(pipeline, seq_iter,
configuration)
seq_list = list(filtered_seq_iter)
assert 'CGAtcgggggg' in str(seq_list[0].seq)
assert len(seq_list) == 6
def main():
'The main part of the script'
in_fhands, out_fhand, pipeline, libraries = set_parameters()
#get seqvars from sam pileup
seq_vars_with_context = snv_contexts_in_sam_pileup(in_fhands,
libraries=libraries)
#filter/clean seq_vars
if pipeline is not None:
seq_vars_with_context = _pipeline_builder(pipeline, seq_vars_with_context)
#remove context to the snv iterator
#print seq_vars_with_context.next()
seq_vars = (snv[0] for snv in seq_vars_with_context if snv is not None)
for snv in seq_vars:
if snv is not None:
out_fhand.write(repr(snv))
