jasonsahl

#!/usr/bin/env python

"""calculates MLST types from assemblies using BLAST.
If the gene is truncated, it will report a "T" and if
the gene has no blast hit, it will report a "X".
Your reference allele names must all end in "fasta"
and must contain a "_" between gene name and number.
The only external dependency is blast+ - tested version
is 2.2.31"""

jasonsahl

#!/usr/bin/env python
"""parse frequencies from a Kmer matrix"""

from __future__ import division
import sys
import os
import optparse
from optparse import OptionParser
from collections import deque

jasonsahl

#!/usr/bin/env python

#A python implementation of building clusters from MASH distances

import optparse
import sys
from optparse import OptionParser
try:
    from scipy.cluster.hierarchy import weighted
    import scipy.spatial.distance as ssd

jasonsahl

#!/usr/bin/env python

import sys
from sys import argv

try:
    out_matrix = open("transposed_matrix.matrix", "w")
    reduced = []
    with open(argv[1]) as my_file:
        for line in my_file: