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Minor tweaks #2

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merged 2 commits into from
Apr 17, 2023
Merged

Minor tweaks #2

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b7e5a0c
Add --valenca-csv option, include CST subtypes in help output
boulund Apr 13, 2023
1dd36b6
Sort CST types in error messages, bump version
boulund Apr 13, 2023
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47 changes: 25 additions & 22 deletions valody.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
"""
__author__ = "Luisa W. Hugerth, Fredrik Boulund"
__date__ = "2023-04"
__version__ = "0.2"
__version__ = "0.2.1"

from pathlib import Path
import argparse
Expand Down Expand Up @@ -51,22 +51,25 @@ def parse_args():
epilog=f"Version v{__version__}",
)

parser.add_argument("-i", "--input", required=True ,
help="Path to VALENCIA output.")
parser.add_argument( "-m", "--metadata",
help="CSV file with 'sampleID,subjectID,menses', where menses takes 1 for yes and 0 for no")
parser.add_argument("-i", "--input", "--valencia-csv",
dest="valencia_csv", metavar="VALENCIA", required=True,
help="Path to VALENCIA output.")
parser.add_argument( "-m", "--metadata-csv",
help="Metadata CSV file with 'sampleID,subjectID,menses', where menses takes 1 for yes and 0 for no.")
parser.add_argument( "-o", "--output",
default="valody.out.csv",
help="Output csv filename [%(default)s].")
default="valody.out.csv",
help="Output csv filename [%(default)s].")
parser.add_argument("-s", "--subtypes", action="store_true",
default=False,
help="Use CST subtypes instead of main types; requires eubiosis and dysbiosis argument")
default=False,
help="Use CST subtypes instead of main types; requires eubiosis and dysbiosis arguments "
"and must define all of the following subtypes as either eubiosis or dysbiosis: "
f"{', '.join(ALL_SUBTYPE_CSTs)}.")
parser.add_argument("-d", "--dysbiosis",
default="III,IV-A,IV-B,IV-C",
help="Comma-separated list of CST or sub-CST considered dysbiotic [%(default)s].")
default="III,IV-A,IV-B,IV-C",
help="Comma-separated list of CST or sub-CST considered dysbiotic [%(default)s].")
parser.add_argument("-e", "--eubiosis",
default="I,II,V",
help="Comma-separated list of CST or sub-CST considered eubiotic [%(default)s].")
default="I,II,V",
help="Comma-separated list of CST or sub-CST considered eubiotic [%(default)s].")

if len(sys.argv) < 2:
parser.print_help()
Expand Down Expand Up @@ -126,16 +129,16 @@ def validate_csts(eubiosis, dysbiosis, subtypes=False):

cst_both_eu_and_dys = eu_cst.intersection(dys_cst)
if cst_both_eu_and_dys:
print(f"A CST cannot be eubiotic and dysbiotic at once: {cst_both_eu_and_dys}")
print(f"A CST cannot be eubiotic and dysbiotic at once: {sorted(cst_both_eu_and_dys)}")
sys.exit(1)

if subtypes:
if all_cst != set(ALL_SUBTYPE_CSTs):
print(f"ERROR: When using subtypes, the following CSTs must be included: {ALL_SUBTYPE_CSTs}")
print(f"ERROR: When using subtypes, the following CSTs must be included: {sorted(ALL_SUBTYPE_CSTs)}")
sys.exit(1)
else:
if all_cst != set(ALL_CSTs):
print(f"ERROR: The following CST must be included: {ALL_CSTs}")
print(f"ERROR: The following CST must be included: {sorted(ALL_CSTs)}")
sys.exit(1)

return eu_cst, dys_cst
Expand All @@ -152,15 +155,15 @@ def check_sampleid_overlaps(metadata, valencia):
only_meta = all_meta_ids.difference(all_val_ids)
only_val = all_val_ids.difference(all_meta_ids)
if len(only_meta) > 0:
print(f"WARNING: {len(only_meta)} sampleIDs in metadata not found in the Valencia table!")
print(f"WARNING: {len(only_meta)} sampleIDs in metadata not found in the VALENCIA table!")
if len(only_val) > 0:
print(f"WARNING: {len(only_val)} sampleIDs in VALENCIA output not found in the metadata!")


def main(input, metadata, eubiosis, dysbiosis, subtypes):
def main(valencia_csv, metadata_csv, eubiosis, dysbiosis, subtypes):
# Step 1: read the Valencia output and store type for each sample
try:
valencia = pd.read_csv(input, sep=",")
valencia = pd.read_csv(valencia_csv, sep=",")
except Exception as e:
print(e)
print(f"ERROR: Unable to load VALENCIA output."
Expand All @@ -169,7 +172,7 @@ def main(input, metadata, eubiosis, dysbiosis, subtypes):

# Step 2: read the metadata file
try:
metadata = pd.read_csv(metadata, sep=",")
metadata = pd.read_csv(metadata_csv, sep=",")
except Exception as e:
print(e)
print(f"ERROR: Unable to load metadata."
Expand Down Expand Up @@ -197,8 +200,8 @@ def main(input, metadata, eubiosis, dysbiosis, subtypes):
print(f"WARNING: Overwriting output file: {args.output}")

main(
args.input,
args.metadata,
args.valencia_csv,
args.metadata_csv,
args.eubiosis,
args.dysbiosis,
args.subtypes,
Expand Down