--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/tarean/kmer_counting.py	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,111 @@
+#!/usr/bin/env python3
+
+import logging
+logger = logging.getLogger(__name__)
+import itertools
+import os
+import sys
+import random
+import sqlite3
+import subprocess
+import shlex  # for command line arguments split
+import operator
+
+REQUIRED_VERSION = (3, 4)
+MAX_PRINT = 10
+MEGABLAST = "-task megablast"
+HITSORT = "-task megablast"
+
+if sys.version_info < REQUIRED_VERSION:
+    raise Exception("\n\npython 3.4 or higher is required!\n")
+
+# additional functions
+
+
+class Sequence:
+
+    def __init__(self, seq, name="", paired=False):
+        # the mode os seq storage can be changed later to make it more
+        # memory efficient
+        self._seq = bytes(str(seq), "ascii")
+        self.name = str(name)
+
+    @property
+    def seq(self):
+        return self._seq.decode("utf-8")
+
+    @seq.setter
+    def seq(self, value):
+        self._seq = bytes(str(value), "ascii")
+
+    def __str__(self):
+        return "{0} : {1}".format(self.name, self.seq)
+
+    @staticmethod
+    def read_fasta(fasta_file_name):
+        '''
+        generator - reads sequences from fasta file
+        return sequence one by one
+        '''
+        with open(fasta_file_name, 'r') as f:
+            header = None
+            seqstr = None
+            for rawline in f:
+                line = rawline.strip()
+                if line == "":
+                    continue
+                if line[0] == ">":
+                    if header and seqstr:
+                        yield Sequence(seqstr, header)
+                        # reset
+                        seqstr = None
+                        header = line[1:]
+                    elif seqstr:
+                        Warning("sequence was not preceeded by header")
+                    else:
+                        header = line[1:]
+                else:
+                    seqstr = line if not seqstr else seqstr + line
+        # skip empty lines:
+        if header and seqstr:
+            yield Sequence(seqstr, header)
+        return
+
+    def write2fasta(self, file_object):
+        file_object.write(">{0}\n{1}\n".format(self.name, self.seq))
+
+
+def get_kmers(string, width=11):
+    L = len(string)
+    parts = [string[i:i + width] for i in range(L - width + 0)]
+    return parts
+
+
+def count_kmers_from_file(f, width=11):
+    counts = {}
+    for i in Sequence.read_fasta(f):
+        a = get_kmers(i.seq, width)
+        for km in a:
+            if "N" in km:
+                continue
+            if km in counts:
+                counts[km] += 1
+            else:
+                counts[km] = 1
+    sorted_counts = sorted(counts.items(),
+                           key=operator.itemgetter(1),
+                           reverse=True)
+    return sorted_counts
+
+
+if __name__ == "__main__":
+    L = len(sys.argv) - 1
+    kmer_length = int(sys.argv[-1])
+    files = sys.argv[1:-1]
+    for fin in files:
+        counts = count_kmers_from_file(fin, kmer_length)
+        fout = "{}_{}.kmers".format(fin, kmer_length)
+        with open(fout, "w") as f:
+            for i in counts:
+                f.write("{}\t{}\n".format(*i))
+        print(fout)