figwig 0.1.0__py3-none-any.whl

figwig/__init__.py

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+# __init__.py
+# Contact: Jacob Schreiber <jmschreiber91@gmail.com>
+
+__version__ = '0.1.0'
+
+from .bigwig import BigWigReader
+from .bigwig import read_bigwig
+from .writer import BigWigWriter
+from .writer import write_bigwig
+
+__all__ = ['BigWigReader', 'read_bigwig', 'BigWigWriter', 'write_bigwig']

figwig/__main__.py

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+# __main__.py
+# Contact: Jacob Schreiber <jmschreiber91@gmail.com>
+
+"""
+The `figwig` command, also run as `python -m figwig`. `figwig bam2bw`
+converts SAM/BAM files or BED/tsv files of fragments into per-base bigWig
+tracks (see `figwig.bam2bw`), and `figwig install-skill` installs figwig's
+Claude Code skill (see `figwig.install_skill`).
+"""
+
+import sys
+import argparse
+
+
+def _parser():
+	from . import __version__
+
+	parser = argparse.ArgumentParser(prog='figwig',
+		description='The commands of figwig, a reader and writer of bigWig files.')
+	parser.add_argument('--version', action='version',
+		version='figwig {}'.format(__version__))
+
+	commands = parser.add_subparsers(dest='command', metavar='command',
+		required=True)
+	commands.add_parser('bam2bw', help="Convert SAM/BAM or BED/tsv files into "
+		"per-base bigWig tracks of reads' 5' ends; see figwig bam2bw -h.")
+
+	install = commands.add_parser('install-skill', help="Install figwig's "
+		"Claude Code skill into a skills directory.", description="Copy "
+		"figwig's Claude Code skill, which teaches a coding agent how to read "
+		"and write bigWigs with figwig, into DIRECTORY/figwig.")
+	install.add_argument('-d', '--directory', default=None, help="The skills "
+		"directory to install into. Default is ~/.claude/skills.")
+	install.add_argument('--symlink', action='store_true', help="Link to the "
+		"skill inside the installed package instead of copying it, so that "
+		"edits to the package show up at once; the link breaks if the package "
+		"moves or is uninstalled.")
+	install.add_argument('-f', '--force', action='store_true', help="Remove "
+		"whatever is at the destination first, such as the skill of an older "
+		"figwig.")
+	return parser
+
+
+def main(argv=None):
+	argv = sys.argv[1:] if argv is None else list(argv)
+
+	# A command's own arguments are parsed by the command, so that its usage
+	# and errors are its own.
+	if len(argv) > 0 and argv[0] == 'bam2bw':
+		from . import bam2bw
+		bam2bw.main(argv[1:], prog='figwig bam2bw', fast_exit=True)
+		return
+
+	args = _parser().parse_args(argv)
+	if args.command == 'install-skill':
+		from . import install_skill
+		install_skill.run(args)
+
+
+if __name__ == '__main__':
+	main()