transdecoder.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 fix_fasta(trinity_fasta,trinity_dir,sra):
# insert SRR before 
	#os.chdir(trinity_dir)
	trinity_out=trinity_dir+sra+".Trinity.fixed.fa"
	fix="""
sed -e "s/^>/>{}_/" {} | sed 's_|_-_g' | sed "s/\s.*$//" > {}
""".format(sra,trinity_fasta,trinity_out,trinity_out,trinity_out)
	#print fix
        #s=subprocess.Popen(fix,shell=True)
	#s.wait()
	#os.chdir("/home/ubuntu/MMETSP/")
	return trinity_out

def transdecoder_LongOrf(transdecoderdir,trinity_fasta):
	os.chdir(transdecoderdir)
	print os.getcwd()
        print os.path.isfile(trinity_fasta)
	if os.path.isfile(trinity_fasta):
		print "file exists:",trinity_fasta
		trans_command="""
/home/ubuntu/TransDecoder-3.0.0/TransDecoder.LongOrfs -t {} -m 100
""".format(trinity_fasta)
		print trans_command	
		s=subprocess.Popen(trans_command,shell=True)
		s.wait()
		print "Transdecoder finished."
	os.chdir("/home/ubuntu/MMETSP/")

def transdecoder_Predict(transdecoderdir,trinity_fasta_prefix):
	os.chdir(transdecoderdir)
	print os.getcwd()
	print os.path.isfile(trinity_fasta_prefix)
	trans_predict_command="""
/home/ubuntu/TransDecoder-3.0.0/TransDecoder.Predict -t {}
""".format(trinity_fasta_prefix)
	print trans_predict_command
	s=subprocess.Popen(trans_predict_command,shell=True)
        s.wait()
	os.chdir("/home/ubuntu/MMETSP/")

def get_longest_ORF(transdecoderdir,trinity_fasta):
        os.chdir(transdecoderdir)
        print os.getcwd()
        print os.path.isfile(trinity_fasta+".transdecoder.pep")
        get_longest_orf_command="""
/home/ubuntu/TransDecoder-3.0.0/util/get_longest_ORF_per_transcript.pl {}.transdecoder.pep > {}.transdecoder.pep.longest.pep
""".format(trinity_fasta,trinity_fasta)
        print get_longest_orf_command
        s=subprocess.Popen(get_longest_orf_command,shell=True)
        s.wait()
        os.chdir("/home/ubuntu/MMETSP/")

def fix(transdecoderdir,trinity_fasta,sra,new_trinity_fasta):
        os.chdir(transdecoderdir)
        fix_command="""
sed -e 's/>.*::SRR/>SRR/' {}{}.transdecoder.pep.longest.pep | sed -e 's/::.*//' | sed 's/\*//g'i > {}{}.Trinity.pep.longest
""".format(transdecoderdir,trinity_fasta,new_trinity_fasta,sra)
        print fix_command
        s=subprocess.Popen(fix_command,shell=True)
        s.wait()
        os.chdir("/home/ubuntu/MMETSP/")

def copy_files(trinity_file,trinity_fasta,transdecoderdir,sra):
	copy_command="cp "+transdecoderdir+sra+".Trinity.fixed.fa.transdecoder.pep.longest.pep"+" "+"/home/ubuntu/MMETSP/mmetsp_trinity_finished/"
        print copy_command
	#copy_command="cp "+trinity_file+" "+transdecoderdir+trinity_fasta
        #print copy_command
        #rm_command="rm -rf "+transdecoderdir+trinity_fasta+".transdecoder_dir"
	#print rm_command
	#s=subprocess.Popen(copy_command,shell=True)
        #s.wait()

def execute(basedir,url_data):
	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/"
			transdecoderdir=newdir+"transdecoder/"
			clusterfunc.check_dir(transdecoderdir)
			trinity_in_fasta=trinitydir+"Trinity.fasta"
			#trinity_fasta_prefix=sra+".Trinity.fa"
			trinity_fasta_prefix=sra+".Trinity.fixed.fa"
                        trinity_fasta=fix_fasta(trinity_in_fasta,trinitydir,sra)
			#copy_files(trinity_fasta,trinity_fasta_prefix,transdecoderdir)
			#transdecoder_LongOrf(transdecoderdir,trinity_fasta_prefix)
			#transdecoder_Predict(transdecoderdir,trinity_fasta_prefix)
			#get_longest_ORF(transdecoderdir,trinity_fasta_prefix)
			#new_trinity_fasta="/mnt/mmetsp_trinity_finished/"
                        #clusterfunc.check_dir(new_trinity_fasta)
                        #fix(transdecoderdir,trinity_fasta_prefix,sra,new_trinity_fasta)
                        copy_files(trinity_fasta_prefix,trinity_fasta,transdecoderdir,sra)




file_locations={"/mnt2/mmetsp/":"MMETSP_SRA_Run_Info_subset_d.csv",
		"/mnt3/mmetsp/":"MMETSP_SRA_Run_Info_subset_a.csv",
		"/mnt4/mmetsp/":"MMETSP_SRA_Run_Info_subset_b.csv"}

for basedir in file_locations.keys():	
	datafile=file_locations[basedir]
	url_data=get_data(datafile)
	print url_data
	execute(basedir,url_data)