dammit.py

import os
import os.path
from os.path import basename
from urllib import urlopen
from urlparse import urlparse
import subprocess
from subprocess import Popen, PIPE
import urllib
import shutil
import glob
# custom Lisa module
import clusterfunc


def get_data(thefile):
    count=0
    url_data={}
    with open(thefile,"rU") as inputfile:
        headerline=next(inputfile).split(',')
        #print headerline        
        position_name=headerline.index("ScientificName")
        position_reads=headerline.index("Run")
        position_ftp=headerline.index("download_path")
        for line in inputfile:
            line_data=line.split(',')
            name="_".join(line_data[position_name].split())
            read_type=line_data[position_reads]
            ftp=line_data[position_ftp]
            name_read_tuple=(name,read_type)
            print name_read_tuple
            #check to see if Scientific Name and run exist
            if name_read_tuple in url_data.keys():
                #check to see if ftp exists
                if ftp in url_data[name_read_tuple]:
                    print "url already exists:", ftp
                else:
                    url_data[name_read_tuple].append(ftp)
            else:
                url_data[name_read_tuple] = [ftp]
        return url_data

def dammit_string(basedir,dammitdir,SRA,trinity_fasta):
	j="""
dammit annotate {} --busco-group eukaryota --database-dir /mnt/dammit_databases --n_threads 8
""".format(trinity_fasta)
	dammitfile=dammitdir+SRA+".dammit.sh"
	os.chdir(dammitdir)
	with open(dammitfile,"w") as dammitfilewrite:
		dammitfilewrite.write(j)
	print "File written:",dammitfile
	s=subprocess.Popen("sudo bash "+dammitfile,shell=True)
	s.wait()
	os.chdir(basedir)
	
def execute(url_data,basedir):
	for item in url_data.keys():
		organism=item[0]
		org_seq_dir=basedir+organism+"/"
		url_list=url_data[item]
		for url in url_list:
			sra=basename(urlparse(url).path)
			newdir=org_seq_dir+sra+"/"
			trinitydir=newdir+"trinity/trinity_out/"
			dammitdir=newdir+"dammit_dir/"
			clusterfunc.check_dir(dammitdir)
			trinity_fasta=trinitydir+"Trinity.fasta"
			print trinity_fasta
			if os.path.isfile(trinity_fasta):
				print "File exists:",trinity_fasta
				dammit_string(basedir,dammitdir,sra,trinity_fasta)

basedir="/mnt/mmetsp/"
datafile="MMETSP_SRA_Run_Info_subset2.csv"
url_data=get_data(datafile)
print url_data
execute(url_data,basedir)