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Shorten filenames #117

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merged 5 commits into from
Aug 4, 2016
Merged

Shorten filenames #117

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fe8a692
Shorten reference_data test filenames
martinghunt Aug 4, 2016
b67ce5f
Shorten samtools_variants test filenames
martinghunt Aug 4, 2016
bec9a97
Shorten assembly_variants test filenames
martinghunt Aug 4, 2016
3564faa
Shorten clusters_test test filenames
martinghunt Aug 4, 2016
3b4221c
Shorten cluster_test test filenames
martinghunt Aug 4, 2016
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12 changes: 6 additions & 6 deletions ariba/tests/assembly_variants_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,10 +102,10 @@ def test_filter_mummer_variants(self):
self.assertEqual(expected, mummer_variants)


def test_get_one_variant_for_one_contig_non_coding(self):
def test_one_var_one_ctg_noncdg(self):
'''test _get_one_variant_for_one_contig_non_coding'''
fasta_in = os.path.join(data_dir, 'assembly_variants_test_get_variants_non_coding.fa')
tsv_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv')
fasta_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_noncdg.fa')
tsv_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_noncdg.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
ref_sequence_name = 'non_coding'
refdata_var_dict = refdata.metadata[ref_sequence_name]
Expand Down Expand Up @@ -144,10 +144,10 @@ def test_get_one_variant_for_one_contig_non_coding(self):
self.assertEqual(expected_used_variants[i], got_used_variants)


def test_get_one_variant_for_one_contig_coding(self):
def test_one_var_one_ctg_cdg(self):
'''test _get_one_variant_for_one_contig_coding'''
fasta_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa')
tsv_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv')
fasta_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_cdg.fa')
tsv_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_cdg.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
ref_sequence_name = 'presence_absence'
ref_sequence = refdata.sequence(ref_sequence_name)
Expand Down
94 changes: 48 additions & 46 deletions ariba/tests/cluster_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -216,9 +216,9 @@ def test_full_run_ok_variants_only_variant_not_present(self):
def test_full_run_ok_variants_only_variant_not_present_always_report(self):
'''test complete run of cluster on a variants only gene when variant not present but always report variant'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only.not_present.always_report.metadata.tsv')
tsv_in = os.path.join(data_dir, 'cluster_full_run_varonly.not_present.always_report.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_variants_only.not_present.always_report'
tmpdir = 'tmp.cluster_full_run_varonly.not_present.always_report'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir)

c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=66, total_reads_bases=3300)
Expand Down Expand Up @@ -265,13 +265,13 @@ def test_full_run_ok_gene_start_mismatch(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_pres_abs_gene(self):
def test_full_run_smtls_snp_presabs_gene(self):
'''test complete run where samtools calls a snp in a presence/absence gene'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_gene'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
Expand All @@ -281,13 +281,15 @@ def test_full_run_ok_samtools_snp_pres_abs_gene(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_var_only_gene(self):
def test_full_run_smtls_snp_varonly_gene_2(self):
'''test complete run where samtools calls a snp in a variant only gene'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv')
# _2 because I think test_full_run_smtls_snp_varonly_gene tests the asame functionality.
# ... but let's leave both tests in anyway
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_gene'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene'), tmpdir)
tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_gene_2'
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
Expand All @@ -297,13 +299,13 @@ def test_full_run_ok_samtools_snp_var_only_gene(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_pres_abs_gene(self):
def test_full_run_known_smtls_snp_presabs_gene(self):
'''test complete run where samtools calls a snp at a known snp location in a presence/absence gene'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand All @@ -316,13 +318,13 @@ def test_full_run_ok_samtools_snp_known_position_pres_abs_gene(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var(self):
def test_full_run_smtls_snp_varonly_gene_no_snp(self):
'''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var'), tmpdir)
tmpdir = 'tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp'
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand All @@ -335,13 +337,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var(self):
def test_full_run_smtls_snp_varonly_gene(self):
'''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand All @@ -354,13 +356,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var(sel
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_pres_abs_noncoding(self):
def test_full_run_smtls_snp_presabs_nonc(self):
'''test complete run where samtools calls a snp in a presence/absence noncoding sequence'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding'), tmpdir)
tmpdir = 'tmp.cluster_test_full_run_smtls_snp_presabs_nonc'
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
Expand All @@ -370,13 +372,13 @@ def test_full_run_ok_samtools_snp_pres_abs_noncoding(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_var_only_noncoding(self):
def test_full_run_smtls_snp_varonly_nonc(self):
'''test complete run where samtools calls a snp in a presence/absence noncoding sequence'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_noncoding'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding'), tmpdir)
tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_nonc'
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
Expand All @@ -386,13 +388,13 @@ def test_full_run_ok_samtools_snp_var_only_noncoding(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding(self):
def test_full_run_known_smtls_snp_presabs_nonc(self):
'''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand All @@ -405,13 +407,13 @@ def test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding(self):
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var(self):
def test_full_run_smtls_snp_varonly_nonc_no_snp(self):
'''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand All @@ -424,13 +426,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_hav
shutil.rmtree(tmpdir)


def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var(self):
def test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc(self):
'''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var'''
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv')
fasta_in = os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.fa')
tsv_in = os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding'
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var'), tmpdir)
shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()

Expand Down
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