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Public init v2 #712

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Public init v2 #712

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7df46bb
adding back public-init, this time with the option to specify the Sra…
mortonjt Jan 1, 2024
fc80d01
fixing file issues
mortonjt Jan 1, 2024
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4 changes: 2 additions & 2 deletions atlas/atlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

from snakemake.io import load_configfile
from .make_config import validate_config
from .init.atlas_init import run_init # , run_init_sra
from .init.atlas_init import run_init, run_init_sra

from .__init__ import __version__

Expand Down Expand Up @@ -66,7 +66,7 @@ def cli(obj):
cli.add_command(run_init)


# cli.add_command(run_init_sra)
cli.add_command(run_init_sra)


def get_snakefile(file="workflow/Snakefile"):
Expand Down
50 changes: 18 additions & 32 deletions atlas/init/atlas_init.py
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Expand Up @@ -196,7 +196,13 @@ def run_init(
"ERR1190946 PRJEB20796\n\n"
"Reads are automatically downloaded and only temporarily stored on your machine.",
)
@click.argument("identifiers", nargs=-1, type=str)
@click.option(
"-r",
"--run-table",
type=click.Path(dir_okay=True, writable=True, resolve_path=True),
show_default=True,
help="location to the run table",
)
@click.option(
"-d",
"--db-dir",
Expand Down Expand Up @@ -228,20 +234,13 @@ def run_init(
help="Ignore the paired end reads from your SRA samples",
)
def run_init_sra(
identifiers,
run_table,
db_dir,
working_dir,
skip_qc=False,
ignore_paired=False,
overwrite=False,
):
""""""

if len(identifiers) == 0:
click.echo(
"No SRA identifiers supplied, exiting. Use --help for more information."
)
sys.exit(1)

from .get_SRA_runinfo import get_runtable_from_ids
from .parse_sra import (
Expand All @@ -261,32 +260,19 @@ def run_init_sra(

runinfo_file = working_dir / "RunInfo.tsv"

if os.path.exists(runinfo_file) & (not overwrite):
if not ((len(identifiers) == 1) & (identifiers[0].lower() == "continue")):
logger.error(
f"Found Filtered runinfo file {runinfo_file}"
"If you want me to continue with this one use 'continue' instead of identifiers. "
"Alternatively use --overwrite to overwrite the files"
)
sys.exit(1)

else:
logger.info(f"Downloading runinfo from SRA")

# Create runinfo table in folder for SRA reads
runinfo_file_original = SRA_subfolder / "RunInfo_original.tsv"

get_runtable_from_ids(identifiers, runinfo_file_original)
# Create runinfo table in folder for SRA reads
# runinfo_file_original = SRA_subfolder / "RunInfo_original.tsv"
runinfo_file_original = run_table

# Parse runtable
RunTable = load_and_validate_runinfo_table(runinfo_file_original)
# Parse runtable
RunTable = load_and_validate_runinfo_table(runinfo_file_original)

# Filter runtable
RunTable_filtered = filter_runinfo(RunTable, ignore_paired=ignore_paired)
# Filter runtable
RunTable_filtered = filter_runinfo(RunTable, ignore_paired=ignore_paired)

# save filtered runtable
logger.info(f"Write filtered runinfo to {runinfo_file}")
RunTable_filtered.to_csv(runinfo_file, sep="\t")
# save filtered runtable
logger.info(f"Write filtered runinfo to {runinfo_file}")
RunTable_filtered.to_csv(runinfo_file, sep=",")

# validate if can be merged
RunTable = validate_merging_runinfo(runinfo_file)
Expand Down
6 changes: 3 additions & 3 deletions atlas/init/parse_sra.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@


def load_and_validate_runinfo_table(path):
RunTable = pd.read_csv(path, sep="\t", index_col=0)
RunTable = pd.read_csv(path, sep=",", index_col=0)

# validate sra table
format_error = False
Expand All @@ -24,7 +24,7 @@ def load_and_validate_runinfo_table(path):
"LibraryLayout",
"LibrarySource",
"LibrarySelection",
"LibraryStrategy",
#"LibraryStrategy",
"BioSample",
]
for header in Expected_headers:
Expand Down Expand Up @@ -72,7 +72,7 @@ def filter_runinfo(RunTable, ignore_paired=False):
f"Filtered out {Difference} runs"
)

for key in ["LibrarySelection", "LibraryStrategy"]:
for key in ["LibrarySelection"]: #, "LibraryStrategy"]:
Nruns_before = RunTable.shape[0]
All_values = RunTable[key].unique()
if any(RunTable[key] != Expected_library_values[key]):
Expand Down