add genomic variants modules

docs/source/genomic_variants.rst

@@ -0,0 +1,11 @@
+Genomic Variants
+=======================
+
+.. automodule:: genomkit.variants
+    :members:
+
+.. automodule:: genomkit.variants.gvariant
+    :members:
+
+.. automodule:: genomkit.variants.gvariants
+    :members:

docs/source/index.rst

@@ -28,4 +28,5 @@ Contents
    genomic_regions
    genomic_annotation
    genomic_coverage
+   genomic_variants
 

genomkit/__init__.py

@@ -5,5 +5,7 @@
 from .annotation.gannotation import GAnnotation
 from .alignments.galignments import GAlignments
 from .coverages.gcoverages import GCoverage
+from .variants.gvariant import GVariant
+from .variants.gvariants import GVariants
 
 __version__ = "0.2.4"

genomkit/variants/__init__.py

@@ -0,0 +1,9 @@
+"""
+Genomic Variants Modules
+
+These modules contain functions and classes for working with genomic variants.
+It provides utilities for handling and analyzing genomic variants.
+
+- **GVariants** is a collection of many genomic variants.
+- **GVariantsSet** is a set of many GVariants which represent different genomic variants.
+"""

genomkit/variants/gvariant.py

@@ -0,0 +1,21 @@
+class GVariant:
+    __slot__ = ["chrom", "pos", "vid", "ref", "alt", "qual", "filter_status",
+                "info"]
+
+    def __init__(self, chrom: str, pos: int, vid: str, ref: str, alt: str,
+                 qual: int, filter_status: str, info: str = []):
+        self.chrom = chrom
+        self.pos = pos
+        self.vid = vid
+        self.ref = ref
+        self.alt = alt
+        self.qual = qual
+        self.filter_status = filter_status
+        self.info = info
+
+    def to_GRegion(self):
+        from genomkit import GRegion
+        region = GRegion(sequence=self.chrom, start=self.pos, end=self.pos,
+                         name=self.vid, data=[self.ref, self.alt, self.qual,
+                                              self.filter_status] + self.info)
+        return region

genomkit/variants/gvariants.py

@@ -0,0 +1,63 @@
+from genomkit import GVariant
+
+
+###########################################################################
+# GVariants
+###########################################################################
+class GVariants:
+    """
+    GVariants module
+
+    This module contains functions and classes for working with a collection of
+    genomic variants. It provides utilities for handling and analyzing the
+    interactions of many genomic variants.
+    """
+    def __init__(self, name: str = "", load: str = ""):
+        """Initiate GVariants object.
+
+        :param name: Define the name, defaults to ""
+        :type name: str, optional
+        :param load: Define the filename for loading a VCF file, defaults to ""
+        :type load: str, optional
+        """
+        self.name = name
+        self.variants = []
+        if load:
+            self.load(filename=load)
+
+    def load(self, filename):
+        """Load variants from a VCF file.
+
+        :param filename: Define the filename for loading a VCF file
+        :type filename: str
+        """
+        with open(filename, 'r') as vcf_file:
+            for line in vcf_file:
+                if line.startswith('#'):
+                    continue  # Skip header lines
+                fields = line.strip().split('\t')
+                chrom = fields[0]
+                pos = int(fields[1])
+                vid = fields[2]
+                ref = fields[3]
+                alt = fields[4]
+                qual = fields[5]
+                filter_status = fields[6]
+                info = fields[7:]
+                variant = GVariant(chrom=chrom, pos=pos, vid=vid, ref=ref,
+                                   alt=alt, qual=qual,
+                                   filter_status=filter_status,
+                                   info=info)
+                self.variants.append(variant)
+
+    def to_GRegions(self):
+        """Convert the GVariants to a GRegions object.
+
+        :return: A GRegions object
+        :rtype: GRegions
+        """
+        from genomkit import GRegions
+        regions = GRegions(name=self.name)
+        for variant in self.variants:
+            regions.add(variant.to_GRegion())
+        return regions