--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RaGOO/ragoo_utilities/PAFReader.py	Mon Jul 26 18:22:37 2021 +0000
@@ -0,0 +1,40 @@
+class PAFLine:
+    """ Object to represent a single alignment in a minimap PAF file. """
+
+    def __init__(self, in_line):
+        """
+        start positions should be before end positions for both query and target
+        """
+        self.line = in_line.rstrip().split('\t')
+        self.contig = self.line[0]
+        self.query_len = int(self.line[1])
+        self.query_start = int(self.line[2])
+        self.query_end = int(self.line[3])
+        self.strand = self.line[4]
+        self.ref_header = self.line[5]
+        self.ref_len = int(self.line[6])
+        self.ref_start = int(self.line[7])
+        self.ref_end = int(self.line[8])
+        self.num_match = int(self.line[9])
+        self.aln_len = int(self.line[10])
+        self.mapq = int(self.line[11])
+
+        assert self.query_start <= self.query_end
+        assert self.ref_start <= self.ref_end
+
+    def __str__(self):
+        return '\t'.join(self.line)
+
+    def __eq__(self, other):
+        return self.line == other.line
+
+
+class PAFReader:
+
+    def __init__(self, paf_file):
+        self.paf_file = paf_file
+
+    def parse_paf(self):
+        with open(self.paf_file) as f:
+            for line in f:
+                yield PAFLine(line)
\ No newline at end of file