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Merge pull request #12 from Center-for-Health-Data-Science/fix11_expe…
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…riment_attributes

recount3 sub-package updated
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@ValeSora
ValeSora authored Jul 18, 2024
2 parents 49848d4 + 8cd0187 commit 82289d2
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Showing 15 changed files with 752 additions and 512 deletions.
182 changes: 149 additions & 33 deletions bulkDGD/execs/_dgd_get_recount3_data_single_batch.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,6 @@ def main():
"The name of the Recount3 project for which samples will " \
f"be retrieved. The available projects are: {ip_choices_str}."
parser.add_argument("-ip", "--input-project-name",
type = str,
required = True,
choices = ip_choices,
help = ip_help)
Expand All @@ -80,7 +79,6 @@ def main():
"associated with." \
"For SRA data, this is the code associated with the project."
parser.add_argument("-is", "--input-samples-category",
type = str,
required = True,
help = is_help)

Expand All @@ -92,7 +90,6 @@ def main():
"written in the working directory. The default file name is " \
"'{input_project_name}_{input_samples_category}.csv'."
parser.add_argument("-o", "--output-csv",
type = str,
default = None,
help = o_help)

Expand All @@ -102,7 +99,6 @@ def main():
"The working directory. The default is the current " \
"working directory."
parser.add_argument("-d", "--work-dir",
type = str,
default = os.getcwd(),
help = d_help)

Expand Down Expand Up @@ -139,19 +135,44 @@ def main():
"accepts a plain text file containing the string " \
"since it can be long for complex queries."
parser.add_argument("-qs", "--query-string",
type = str,
default = None,
help = qs_help)

#-----------------------------------------------------------------#

mk_help = \
"A vertical line (|)-separated list of names of metadata " \
"columns to keep in the final data frame. All the other " \
"metadata columns will be dropped from the data frame. If " \
"neither this option nor the '-md', '--metadata-to-drop' " \
"is passed, all metadata columns are kept in the final data " \
"frame."
parser.add_argument("-mk", "--metadata-to-keep",
default = None,
help = mk_help)

#-----------------------------------------------------------------#

md_help = \
"A vertical line (|)-separated list of names of metadata " \
"columns to drop in the final data frame. All the other " \
"metadata columns will be kept in the final data frame. Use " \
"the '_all_' reserved keyword to drop all metadata columns " \
"from the data frame. If neither this option nor the '-mk', " \
"'--metadata-to-keep' option is passed, all metadata " \
"columns are kept in the final data frame."
parser.add_argument("-md", "--metadata-to-drop",
default = None,
help = md_help)

#-----------------------------------------------------------------#

lf_default = "_dgd_get_recount3_data_single_batch.log"
lf_help = \
"The name of the log file. The file will be written " \
"in the working directory. The default file name is " \
f"'{lf_default}'."
parser.add_argument("-lf", "--log-file",
type = str,
default = lf_default,
help = lf_help)

Expand Down Expand Up @@ -187,6 +208,8 @@ def main():
output_csv = args.output_csv
wd = os.path.abspath(args.work_dir)
query_string = args.query_string
metadata_to_keep = args.metadata_to_keep
metadata_to_drop = args.metadata_to_drop
save_gene_sums = args.save_gene_sums
save_metadata = args.save_metadata
log_file = args.log_file
Expand All @@ -197,7 +220,7 @@ def main():
#-----------------------------------------------------------------#

# Get the module's logger.
logger = log.getLogger(__name__)
logger = log.getLogger("dgd_get_recount3_data")

# Set WARNING logging level by default.
log_level = log.WARNING
Expand All @@ -219,9 +242,11 @@ def main():
handlers = \
util.get_handlers(\
log_console = log_console,
log_console_level = log.ERROR,
log_file_class = log.FileHandler,
log_file_options = {"filename" : log_file},
log_level = log_level)
log_file_options = {"filename" : log_file,
"mode" : "w"},
log_file_level = log_level)

# Set the logging configuration.
log.basicConfig(level = log_level,
Expand All @@ -247,10 +272,8 @@ def main():

# Log it an exit.
errstr = \
"It was not possible to get the RNA-seq data for " \
f"project '{input_project_name}', samples " \
f"'{input_samples_category}' from Recount3. " \
f"Error: {e}"
"It was not possible to get the RNA-seq data from " \
f"Recount3. Error: {e}"
logger.exception(errstr)
sys.exit(errstr)

Expand All @@ -271,14 +294,32 @@ def main():

# Log it an exit.
errstr = \
"It was not possible to get the metadata for " \
f"project '{input_project_name}', samples " \
f"'{input_samples_category}' from Recount3. " \
"It was not possible to get the metadata from Recount3. " \
f"Error: {e}"
logger.exception(errstr)
sys.exit(errstr)

#-----------------------------------------------------------------#

# Try to merge the RNA-seq data frame and the metadata data frame.
try:

df_final = \
recount3.merge_gene_sums_and_metadata(\
df_gene_sums = df_gene_sums,
df_metadata = df_metadata)

# If something went wrong
except Exception as e:

# Log it and exit.
errstr = \
"It was not possible to combine the RNA-seq data " \
f"with the metadata. Error: {e}"
logger.exception(errstr)
sys.exit(errstr)

#-----------------------------------------------------------------#

# If the user has passed a query string or a file containing the
# query string
Expand All @@ -303,20 +344,12 @@ def main():

# Try to add the metadata to the RNA-seq data frame.
try:

# Merge the RNA-seq data frame and the metadata data frame.
df_merged = \
recount3.merge_gene_sums_and_metadata(\
df_gene_sums = df_gene_sums,
df_metadata = df_metadata,
project_name = input_project_name)

# Filter the samples.
df_final = \
recount3.filter_by_metadata(\
df = df_merged,
query_string = query_string,
project_name = input_project_name)
df = df_final,
query_string = query_string)

# If something went wrong
except Exception as e:
Expand All @@ -328,12 +361,95 @@ def main():
logger.exception(errstr)
sys.exit(errstr)

# Otherwise
else:
#-----------------------------------------------------------------#

# If the user passed a list of metadata columns to keep in the
# final data frame
if metadata_to_keep is not None:

# The final data frame will be the one containing the gene
# expression data.
df_final = df_gene_sums
# Get the list of metadata columns to keep.
metadata_to_keep = \
[m.lstrip("'").rstrip("'") for m \
in metadata_to_keep.rstrip().split("|")]

# Get the columns to keep in the final data frame.
columns_to_keep = \
[col for col in df_final.columns \
if col.startswith("ENSG")] + \
[col for col in df_final.columns \
if not col.startswith("ENSG") \
and col in metadata_to_keep]

# Try to keep only the selected columns
try:

df_final = df_final.loc[:,columns_to_keep]

# If something went wrong
except Exception as e:

# Get a string representing the metadata columns to keep.
metadata_to_keep_str = \
", ".join([f"'{m}'" for m in metadata_to_keep])

# Log it and exit.
errstr = \
"It was not possible to keep only the following " \
"metadata columns in the final data frame: " \
f"{metadata_to_keep_str}. Error: {e}"
logger.exception(errstr)
sys.exit(errstr)

#-----------------------------------------------------------------#

# If the user passed a list of metadata columns to drop in the
# final data frame
if metadata_to_drop is not None:

# If the user wants to drop all metadata columns
if metadata_to_drop == "_all_":

# Get the columns to keep in the final data frame.
columns_to_keep = \
[col for col in df_final.columns \
if col.startswith("ENSG")]

# Otherwise
else:

# Get the list of metadata columns.
metadata_to_drop = \
[m.lstrip("'").rstrip("'") for m \
in metadata_to_drop.rstrip().split("|")]

# Get the columns to keep in the final data frame.
columns_to_keep = \
[col for col in df_final.columns \
if col.startswith("ENSG")] + \
[col for col in df_final.columns \
if not col.startswith("ENSG") \
and col not in metadata_to_drop]

# Try to keep only the selected columns.
try:

df_final = df_final.loc[:, columns_to_keep]

# If something went wrong
except Exception as e:

# Get a string representing the metadata columns to
# drop.
metadata_to_drop_str = \
", ".join([f"'{m}'" for m in metadata_to_drop])

# Log it and exit.
errstr = \
"It was not possible to drop the following " \
"metadata columns from the final data frame: " \
f"{metadata_to_drop_str}. Error: {e}"
logger.exception(errstr)
sys.exit(errstr)

#-----------------------------------------------------------------#

Expand Down Expand Up @@ -364,7 +480,7 @@ def main():

# Log it and exit.
errstr = \
"It was not possible to save the RNA-seq data " \
f"in '{output_csv_path}'. Error: {e}"
"It was not possible to save the final data frame in " \
f"'{output_csv_path}'. Error: {e}"
logger.exception(errstr)
sys.exit(errstr)
3 changes: 2 additions & 1 deletion bulkDGD/execs/dgd_get_probability_density.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -198,10 +198,11 @@ def main():
handlers = \
util.get_handlers(\
log_console = log_console,
log_console_level = log_level,
log_file_class = log.FileHandler,
log_file_options = {"filename" : log_file,
"mode" : "w"},
log_level = log_level)
log_file_level = log_level)

# Set the logging configuration.
log.basicConfig(level = log_level,
Expand Down
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