Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MAINT: Removed 'move_files' function from 'reads.py' #25

Merged
merged 4 commits into from
Jan 11, 2024
Merged

MAINT: Removed 'move_files' function from 'reads.py' #25

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
1963544
removed move_files from reads
VinzentRisch Jan 9, 2024
8f4b64f
Update q2_amr/tests/card/test_reads.py
VinzentRisch Jan 11, 2024
5e43625
Revert "Update q2_amr/tests/card/test_reads.py"
VinzentRisch Jan 11, 2024
65695c1
removed empty line after review Santi
VinzentRisch Jan 11, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 13 additions & 13 deletions q2_amr/card/reads.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,13 +74,24 @@ def annotate_reads_card(
path=path_allele, samp_bin_name=samp, data_type="reads"
)
allele_frequency_list.append(allele_frequency)

path_gene = os.path.join(samp_input_dir, "output.gene_mapping_data.txt")
gene_frequency = read_in_txt(
path=path_gene, samp_bin_name=samp, data_type="reads"
)
gene_frequency_list.append(gene_frequency)
move_files(samp_input_dir, samp_allele_dir, "allele")
move_files(samp_input_dir, samp_gene_dir, "gene")

# Move mapping and stats files to the sample allele and gene directories
for map_type, des_dir in zip(
["allele", "gene"], [samp_allele_dir, samp_gene_dir]
):
files = [f"{map_type}_mapping_data.txt", "overall_mapping_stats.txt"]

for file in files:
shutil.copy(
os.path.join(samp_input_dir, "output." + file),
os.path.join(des_dir, file),
)

allele_feature_table = create_count_table(allele_frequency_list)
gene_feature_table = create_count_table(gene_frequency_list)
Expand All @@ -92,17 +103,6 @@ def annotate_reads_card(
)


def move_files(source_dir: str, des_dir: str, map_type: str):
shutil.move(
os.path.join(source_dir, f"output.{map_type}_mapping_data.txt"),
os.path.join(des_dir, f"{map_type}_mapping_data.txt"),
)
shutil.copy(
os.path.join(source_dir, "output.overall_mapping_stats.txt"),
os.path.join(des_dir, "overall_mapping_stats.txt"),
)


def run_rgi_bwt(
cwd: str,
samp: str,
Expand Down
44 changes: 2 additions & 42 deletions q2_amr/tests/card/test_reads.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@
from q2_amr.card.reads import (
annotate_reads_card,
extract_sample_stats,
move_files,
plot_sample_stats,
run_rgi_bwt,
visualize_annotation_stats,
Expand Down Expand Up @@ -147,11 +146,9 @@ def annotate_reads_card_test_body(self, read_type):
# resulting CARD annotation objects
for num in [0, 1]:
map_type = "allele" if num == 0 else "gene"
files = [f"{map_type}_mapping_data.txt", "overall_mapping_stats.txt"]
for samp in ["sample1", "sample2"]:
for file in [
f"{map_type}_mapping_data.txt",
"overall_mapping_stats.txt",
]:
for file in files:
self.assertTrue(
os.path.exists(os.path.join(str(result[num]), samp, file))
)
Expand Down Expand Up @@ -204,43 +201,6 @@ def test_exception_raised(self):
run_rgi_bwt()
self.assertEqual(str(cm.exception), expected_message)

def test_move_files_allele(self):
self.move_files_test_body("allele")

def test_move_files_gene(self):
self.move_files_test_body("gene")

def move_files_test_body(self, map_type):
with tempfile.TemporaryDirectory() as tmp:
source_dir = os.path.join(tmp, "source_dir")
des_dir = os.path.join(
tmp,
"des_dir",
)
os.makedirs(os.path.join(source_dir))
os.makedirs(os.path.join(des_dir))
mapping_data = self.get_data_path(f"output.{map_type}_mapping_data.txt")
mapping_stats = self.get_data_path("output.overall_mapping_stats.txt")
shutil.copy(mapping_data, source_dir)
shutil.copy(mapping_stats, source_dir)
move_files(source_dir, des_dir, map_type)
self.assertTrue(
os.path.exists(
os.path.join(
des_dir,
f"{map_type}_mapping_data.txt",
)
)
)
self.assertTrue(
os.path.exists(
os.path.join(
des_dir,
"overall_mapping_stats.txt",
)
)
)

def test_extract_sample_stats(self):
with tempfile.TemporaryDirectory() as tmp:
mapping_stats_path = self.get_data_path("output.overall_mapping_stats.txt")
Expand Down