brevans

#!/usr/bin/env python
'''
example:
./gen_bowtie2_coms.py fastq_dir bin_dir out_dir

-all sample fastq files must be in on directory
-the bin directory should have samtools and bowtie2
-the outdir must already exist

This script prints the commands to screen.  You can save them to a file with

brevans

#!/usr/bin/env python
from os import path
from glob import iglob
import re
trans = {'AGO':'DAR', 'CAZ':'GUN', 'CF':'CF', 'F':'CF', 
'CRU':'POR', 'ESP':'HOO', 'LG':'ABI', 'LP':'VIC', 
'LT':'VIC', 'PBL':'PBL', 'PBR':'PBR', 'PZ':'EPH', 
'SCR':'CHA', 'VA':'VAN', 'VD':'MIC'}

for fi in iglob('consensus/*.fa'):

brevans

library("SNPolisher")

cwd <- getwd()
summ <- file.path(cwd,"AxiomGT1.summary.txt")
conf <- file.path(cwd,"AxiomGT1.confidences.txt")
post <- file.path(cwd,"AxiomGT1.snp-posteriors.txt")
call <- file.path(cwd,"AxiomGT1.calls.txt")

# Ps_Metrics
ps.metrics <- Ps_Metrics(posteriorFile=post,

brevans

library("adegenet")
library("rgl")
library("phangorn")
library("ape")

setwd("C:/Users/ben/Desktop/temp/pca")
#Read in the data
X <- read.PLINK("pca6.raw", parallel=FALSE)

col <- rainbow(length(levels(pop(X))), start=.3, end=.1)

brevans

#!/usr/bin/env python
from os import path, makedirs, remove, stat
import argparse
import re
from glob import iglob
from collections import defaultdict as dd
from Bio import SeqIO
import vcf

AMB = {'AC': 'M', 'AG': 'R', 'AT': 'W', 'CG': 'S', 'CT': 'Y', 'GT': 'K',

brevans

Keybase proof

I hereby claim:

• I am brevans on github.
• I am benevans (https://keybase.io/benevans) on keybase.
• I have a public key whose fingerprint is 9247 52CE 3718 C27F A5FC 2BAE 102B C92B 8CBF 0EF1

To claim this, I am signing this object:

brevans

#!/usr/bin/env python
import gzip
import sys
from glob import glob
from os.path import basename
import re
from Bio import SeqIO

def gopen(fi, *args, **kwargs):
    if fi.endswith('.gz'):

brevans

#!/usr/bin/env python
import sys
import re
import random
import argparse
from os import makedirs
from glob import glob
import os.path as path
from collections import defaultdict as dd
from Bio import SeqIO

brevans

#!/usr/bin/env python
import csv
import re
import sys
from collections import OrderedDict as od

def translate(annots, gt_row):
    #uses annotation file to translate from 0/1/2/-1 to ACGT
    ps_id = gt_row[0]
    t_gts = []

brevans

#!/usr/bin/env python
from datetime import datetime
import os
from glob import glob

#set up columns
interaction_columns = ['Time_of_Day', 'Time_Stamp', 'Initiator_ID', 
               'Interaction_Number', 'Data_Type', 'Partner_ID', 
               'Initiator_Stake', 'Initiator_X', 'Initiator_Y',
               'Partner_Stake', 'Partner_X', 'Partner_Y', 'Females_Present',