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:

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

"""retrieve only parsimony infomative
sites from a nucleotide multiple sequence alignment"""

from optparse import OptionParser
import sys
try:
    from Bio import SeqIO
except:

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

"""Read counts across a set of reference sequences.
Requires Python 2.7 to run"""

from __future__ import division
from __future__ import print_function
from optparse import OptionParser
import sys
import os

jasonsahl

ERR319438
ERR360775
ERR360792
ERR360848
ERR360746
ERR360782
ERR360788
ERR360789
ERR360783
ERR360770

jasonsahl

#!/usr/bin/env python

"""Transform ribotype data. Input matrix
is a transposed output from bac_seq"""

from __future__ import print_function
from __future__ import division
import sys
import os
import optparse

jasonsahl

#!/usr/bin/python
#parses sequence lengths from a file and prints them to the screen
#usage python seqlength.py infasta
from __future__ import print_function
from sys import argv
import sys
try:
    from Bio import SeqIO
except:
    print("script requires BioPython to run..exiting")

jasonsahl

#The input is two colums: x and corresponding y values
require(MASS) ## for mvrnorm()
set.seed(1)
mine <- read.table("xy.txt")
mine <- data.frame(mine)
names(mine) <- c("X","Y")
plot(mine)
res <- resid(mod <- lm(Y ~ X, data = mine))
res.qt <- quantile(res, probs = c(0.001,0.999))
want <- which(res >= res.qt[1] & res <= res.qt[2])