ShaiberAlon

import os
import sys
import time
import xml.dom.minidom
import string
import getpass

def still_running(job_name, job_owner):
    f=os.popen('qstat -u \* -xml -r')

ShaiberAlon

#!bin/bash
# remove_duplicate_sequence.shx is a short bash to remove multiple copies of sequences from an input fasta file and saves the result in an output fasta file.
# the bash script was based on Pierre Lindenbaum's script: https://www.biostars.org/p/3003/#3008
# input:
# -f | --file  : fasta file
# -o | --output : output file after removing all the sequences
#
while [ "$1" != "" ]; do
        case $1 in
                -f | --file ) shift

ShaiberAlon

#!bin/bash
#
# expects tab-delimited table with only two columns and no header
# column 1 - name of each sequence
# column 2 - sequence
# performs two actions:
# Adds > at the begining of each row
# converts all the tabs to new lines
#
while [ "$1" != "" ]; do

ShaiberAlon

tr  '\r' '\n' < file.txt > file_fix.txt

ShaiberAlon

#!/usr/bin/env python

list1=open('p207_profiled_samples.txt','r')
list2=open('p214_profield_samples.txt','r')

print list(set(list1.read()) - set(list2.read()))

ShaiberAlon

#!/bin/bash

set -e

DIR=Metaphlan_output
job=Metaphlan_Primates
email=alon.shaiber@gmail.com
WAIT () {
    python /workspace/meren/wait_for_cluster.py $1
}

ShaiberAlon

import csv
import numpy as np
import argparse

parser = argparse.ArgumentParser(description='Adding the 2MA column to anvio AA table')
parser.add_argument('-i','--input',metavar='FILE',dest='input_file',help='Input file')
parser.add_argument('-o','--out',metavar='FILE',dest='output_file',help='Name of file for output')
parser.add_argument('-r','--ratio',metavar='NUMBER',dest='ratio',type=float,help='Minimal ratio between consensus and the second most covered amino-acid. If the ratio is lower than the provided threshold, then the 2MA value would be in the form concensus_concensus')
args = parser.parse_args()

ShaiberAlon

#!/usr/bin/env python
# -*- coding: utf-8


__author__ = "Alon Shaiber"
__copyright__ = ""
__credits__ = []
__license__ = ""
__version__ = 1
__maintainer__ = "Alon Shaiber"

ShaiberAlon

#!/usr/bin/env python

import anvio.utils as u
import argparse
import sys
parser =  argparse.ArgumentParser(description='Get nucleotides from fasta file beyween user defined nucleotide positions inside a specified contig')
parser.add_argument('-1','--N1',metavar='INT',dest='n1',type=int,help='Nucleotide sequence start position')
parser.add_argument('-2','--N2',metavar='INT',dest='n2',type=int,help='Nucleotide sequence start position')
parser.add_argument('-c','--contig',metavar='STRING',dest='c',help='Contig name')
parser.add_argument('-o','--out',metavar='FILE',dest='output',help='Output file')

ShaiberAlon

#!/bin/bash

### DEFAULTS (FEEL FREE TO EDIT THESE) ##################
NUM_THREADS_FOR_MAPPING=10
NUM_THREADS_FOR_HMMSCAN=4
NUM_THREADS_FOR_ANVI_GEN_CONTIG=4
NUM_THREADS_FOR_ANVI_PROFILE=4
NUM_THREADS_FOR_ANVI_MERGE=4

# configure whether SNV analysis will be included or not (if you want it included then leave this empty