MutaVerse 0.1.0__tar.gz

mutaverse-0.1.0/MutaVerse/__init__.py

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+from __future__ import absolute_import
+#from . import data
+from .core.simple_seq import *
+from .core.VcfParser import *
+from .core.detect_somatic import *
+
+# Download annotation data
+#download_methyl_anno()
+
+# This is extracted automatically by the top-level setup.py.
+__version__ = '0.0.1'
+__author__ = "Kyle S. Smith"
+
+
+__doc__ = """\
+API
+======
+
+Basic class
+-----------
+
+.. autosummary::
+   :toctree: .
+   
+   SimpleSeq
+"""

mutaverse-0.1.0/MutaVerse/__main__.py

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+import argparse
+from .commandline.commands import run_simple_seq
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    subparsers = parser.add_subparsers()
+
+    # Run SimpleSeq
+    simpleseq_parser = subparsers.add_parser("SimpleSeq")
+    simpleseq_parser.add_argument("--reference_germline", type=str, required=True, help="Reference germline VCF file")
+    simpleseq_parser.add_argument("--fasta", type=str, required=True, help="Reference FASTA file")
+    simpleseq_parser.add_argument("--bam", type=str, required=True, help="Input BAM file")
+    simpleseq_parser.add_argument("--min_reads", type=int, default=2, help="Minimum number of reads to call a variant")
+    simpleseq_parser.add_argument("--min_support", type=int, default=1, help="Minimum number of supporting reads to call a variant")
+    simpleseq_parser.add_argument("--is_bisulfite", action="store_true", help="Whether the data is bisulfite-treated")
+    simpleseq_parser.add_argument("--is_taps", action="store_true", help="Whether the data is TAPS-treated")
+    simpleseq_parser.add_argument("--context", type=str, default="CG", help="Context to consider (CG, CHG, CHH)")
+    simpleseq_parser.add_argument("--keep_cpg", action="store_true", help="Whether to keep CpG sites")
+    simpleseq_parser.add_argument("--keep_chg", action="store_true", help="Whether to keep CHG sites")
+    simpleseq_parser.add_argument("--keep_chh", action="store_true", help="Whether to keep CHH sites")
+    simpleseq_parser.add_argument("--min_frag_len", type=int, default=1, help="Minimum fragment length to consider")
+    simpleseq_parser.add_argument("--max_frag_len", type=int, default=1000, help="Maximum fragment length to consider")
+    simpleseq_parser.add_argument("--output_prefix", type=str, default="output", help="Prefix for output files")
+    simpleseq_parser.add_argument("--require_pair_agreement", action="store_true", help="Whether to require agreement between read pairs")
+    simpleseq_parser.add_argument("--n_threads", type=int, default=1, help="Number of threads to use")
+    simpleseq_parser.set_defaults(func=run_simple_seq)
+
+    args = parser.parse_args()
+
+    args.func(args)

mutaverse-0.1.0/MutaVerse/commandline/__init__.py

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+from . import commands
+
+
+__doc__="""
+Commandline API
+============
+"""

mutaverse-0.1.0/MutaVerse/commandline/commands.py

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+from ..core.simple_seq import SimpleSeq
+
+
+def run_simple_seq(args):
+    SimpleSeq(args.reference_germline, args.bam, args.fasta,
+              min_reads=args.min_reads, min_support=args.min_support,
+              region_chrom=None, is_bisulfite=args.is_bisulfite, is_taps=args.is_taps,
+              require_pair_agreement=args.require_pair_agreement, keep_cpg=args.keep_cpg, context=args.context,
+              keep_chg=args.keep_chg, keep_chh=args.keep_chh,
+              min_frag_len=args.min_frag_len, max_frag_len=args.max_frag_len, 
+              output_prefix=args.output_prefix, n_threads=args.n_threads)
+