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Remove calls to argparse.FileType #27

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Merged
kylebittinger merged 1 commit into from
Mar 23, 2026
Merged

Remove calls to argparse.FileType #27

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16 changes: 10 additions & 6 deletions src/heyfastqlib/command.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import operator
import signal
import sys
from contextlib import nullcontext
from itertools import count
from . import __version__
from .argparse_types import GzipFileType, HFQFormatter
Expand Down Expand Up @@ -157,7 +158,8 @@ def filter_kscore_subcommand(args):


def filter_seq_ids_subcommand(args):
seq_ids = set(parse_seq_ids(args.idsfile))
with open(args.idsfile) as f:
seq_ids = set(parse_seq_ids(f))
counter = {"input_reads": 0, "input_bases": 0, "output_reads": 0, "output_bases": 0}
write_fastq(
args.output,
Expand Down Expand Up @@ -191,8 +193,6 @@ def filter_seq_ids_subcommand(args):
)
fastq_io_parser.add_argument(
"--report",
type=argparse.FileType("w"),
default=sys.stderr,
help="Output report file",
)
fastq_io_parser.add_argument(
Expand Down Expand Up @@ -321,7 +321,6 @@ def heyfastq_main(argv=None):
)
filter_seq_ids_parser.add_argument(
"idsfile",
type=argparse.FileType("r"),
help="File containing sequence ids, one per line",
)
filter_seq_ids_parser.add_argument(
Expand Down Expand Up @@ -370,9 +369,14 @@ def heyfastq_main(argv=None):
for k, v in vars(args).items():
if k not in ("input", "output", "func", "idsfile", "report", "threads"):
report[k] = v

report.update(stats)
json.dump(report, args.report, indent=4)

if args.report is not None:
report_file = open(args.report, "w")
else:
report_file = nullcontext(sys.stderr)
with report_file as f:
json.dump(report, f, indent=4)

# Close all opened files/pipes
for c in closers:
Expand Down
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