kdiverson

OTU  Rank
Otu29838	49.448
Otu29833	45.884
Otu29741	45.536
Otu29878	43.366
Otu29860	42.776
Otu29842	42.67
Otu29835	42.616
Otu29839	42.542
Otu29834	42.528

kdiverson

kdiverson

#!/bin/sh

#script to run digital normalization
#####
#files
R1=$1 #"R1_001" forward fastq reads
R2=$2 #"R2_001" reversed fastq reads
COM=$3 #"combined_001" interleaved reads

#paths

kdiverson

#multi k velvet

seq_file=$1

fq=$(basename $seq_file .trimmed.fq.keep.abundfilt)
for k in {19..51..2};
do
    quicksubmit "velveth && velvetg"

name=$(basename $i .pe.fq.gz);

kdiverson

import sys

def get_next_fasta (fileObject):
	'''usage: for header, seq in get_next_fasta(fileObject):
	'''
	header = ''
	seq = ''
	#The following for loop gets the header of the first fasta
	#record. Skips any leading junk in the file
	for line in fileObject:

kdiverson

#!/usr/bin/python2.7
'''USAGE: quicksubmit.py "command -l parameter" [options]
This script submits your one line command as a job to the pbs job scheduler.
'''
import subprocess as s
import sys
import argparse

def submitjob(job_name, command, subtype = "qsub", walltime = "10:00:00", cput = "10:00:00", pm = "nodes=1:ppn=1:mem=2gb", mailto = "", afterok = "", verbose = False):
    '''USAGE: submitjob('my_job', 'echo "hello world!"')

kdiverson

132585322 (100.00%) were unpaired; of these:
4790404 (3.61%) aligned 0 times
98633353 (74.39%) aligned exactly 1 time
29161565 (21.99%) aligned >1 times
N50: 10038
N90: 100
total contigs: 2097980
average length: 282 bp
trimmed average length: 281 bp
greater than or equal to 100:  1437022

kdiverson

import argparse
import logging

parser = argparse.ArgumentParser()
parser.add_argument('-d','--debug',
    help='Print lots of debugging statements',
    action="store_const",dest="loglevel",const=logging.DEBUG,
    default=logging.WARNING
)
parser.add_argument('-v','--verbose',

kdiverson

hit_total=`awk '{total += $3} END {print total}' *fastsummary.species`
nohit_total=`awk '{total += $2} END {print total}' *nomatchsum`
total=(($hit_total + $nohit_total))
human=`awk '{if ($4==9606) {print $3} }' *fastsummary.species`
echo (($human / $total))

hit_total=`awk '{total += $3} END {print total}' *fastsummary.species`; nohit_total=`awk '{total += $2} END {print total}' *nomatchsum`; total=(($hit_total + $nohit_total)); human=`awk '{if ($4==9606) {print $3} }' *fastsummary.species`; echo (($human / $total))

kdiverson

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
	. ~/.bashrc
fi

# User specific environment and startup programs
# Set colors
export CLICOLOR=1