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transrate_reference.py
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transrate_reference.py
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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
# Python plotting libraries
import pandas as pd
def get_data(thefile):
mmetsp_data={}
with open(thefile,"rU") as inputfile:
headerline=next(inputfile).split(',')
#print headerline
position_name=headerline.index("ScientificName")
position_reads=headerline.index("Run")
position_mmetsp=headerline.index("SampleName")
for line in inputfile:
line_data=line.split(',')
name="_".join(line_data[position_name].split())
read_type=line_data[position_reads]
mmetsp=line_data[position_mmetsp]
test_mmetsp=mmetsp.split("_")
if len(test_mmetsp)>1:
mmetsp=test_mmetsp[0]
name_read_tuple=(name,read_type)
#print name_read_tuple
#check to see if Scientific Name and run exist
if name_read_tuple in mmetsp_data.keys():
#check to see if ftp exists
if mmetsp in mmetsp_data[name_read_tuple]:
print "mmetsp ID already exists:", mmetsp
else:
mmetsp_data[name_read_tuple].append(mmetsp)
else:
mmetsp_data[name_read_tuple] = [mmetsp]
return mmetsp_data
def fix_fasta(trinity_fasta,trinity_dir,sample):
#os.chdir(trinity_dir)
trinity_out=trinity_dir+sample+".Trinity.fixed.fa"
fix="""
sed 's_|_-_g' {} > {}
""".format(trinity_fasta,trinity_out)
#s=subprocess.Popen(fix,shell=True)
#print fix
#s.wait()
#os.chdir("/home/ubuntu/MMETSP/")
return trinity_out
def fix_fasta_reference(mmetsp_assembly,mmetsp_assembly_dir):
mmetsp_assembly_out=mmetsp_assembly_dir+mmetsp_assembly+".fixed.fa"
fix="""
sed 's_|_-_g' {}{} > {}
""".format(mmetsp_assembly_dir,mmetsp_assembly,mmetsp_assembly_out)
#print fix
#s=subprocess.Popen(fix,shell=True)
#s.wait()
return mmetsp_assembly_out
def transrate(transrate_dir,sample,trinity_fasta,mmetsp_assemblies_dir,filename):
transrate_command="""
transrate -o {}{} \\
--assembly {} \\
--reference {} \\
--threads 8
""".format(transrate_dir,sample,trinity_fasta,filename)
print transrate_command
commands = [transrate_command]
process_name = "trans_ref"
module_name_list = ""
filename = sample
#clusterfunc.qsub_file(transrate_dir,process_name,module_name_list,filename,commands)
def transrate_reverse(transrate_dir,sample,trinity_fasta,mmetsp_assemblies_dir,filename):
transrate_command="""
transrate -o {}{} \\
--assembly {} \\
--reference {} \\
--threads 8
""".format(transrate_dir,sample,filename,trinity_fasta)
print "This is the reverse transrate command:"
print transrate_command
commands = [transrate_command]
process_name = "trans_ref_reverse"
module_name_list = ""
filename = sample
#clusterfunc.qsub_file(transrate_dir,process_name,module_name_list,filename,commands)
def parse_transrate_stats(transrate_assemblies):
data=pd.DataFrame.from_csv(transrate_assemblies,header=0,sep=',')
return data
def build_DataFrame(data_frame,transrate_data):
#columns=["n_bases","gc","gc_skew","mean_orf_percent"]
frames=[data_frame,transrate_data]
data_frame=pd.concat(frames)
return data_frame
def get_contigs_data(data_frame,transrate_dir):
listofdirs=os.listdir(transrate_dir)
for dirname in listofdirs:
transrate_dirname=transrate_dir+dirname+"/"
transrate_dirnames=os.listdir(transrate_dirname)
for dirname2 in transrate_dirnames:
if dirname2.endswith(".fixed"):
transrate_contigs=transrate_dirname+dirname2+"/contigs.csv"
if os.path.isfile(transrate_contigs):
print transrate_contigs
data=parse_transrate_stats(transrate_contigs)
data_frame=build_DataFrame(data_frame,data)
else:
print "File missing:",transrate_contigs
return data_frame
def execute(data_frame1,data_frame2,mmetsp_data,basedir,mmetsp_assemblies):
trinity_fail=[]
reference_filename = "blank"
# construct an empty pandas dataframe to add on each assembly.csv to
for item in mmetsp_data.keys():
#print item
organism=item[0]
sample="_".join(item)
org_seq_dir=basedir+organism+"/"
mmetsp_list=mmetsp_data[item]
for mmetsp in mmetsp_list:
print mmetsp
assemblyfileslist=os.listdir(mmetsp_assemblies)
for filename in assemblyfileslist:
if filename.startswith(mmetsp):
if filename.endswith(".fixed.fa"):
print "This is not the one you want."
else:
print "MMETSP assembly found:",filename
reference_filename=filename
if reference_filename == "blank":
print "No MMETSP file found:",mmetsp
break
else:
sra=item[1]
newdir=org_seq_dir+sra+"/"
trinitydir=newdir+"trinity/"
transrate_dir=newdir+"transrate/"
transrate_reference_dir=newdir+"transrate_dib_v_ncgr_cds/"
clusterfunc.check_dir(transrate_reference_dir)
transrate_reverse_dir=newdir+"transrate_ncgr_cds_v_dib/"
clusterfunc.check_dir(transrate_reverse_dir)
trinity_fasta=trinitydir+sample+".Trinity.fixed.fasta"
if os.path.isfile(trinity_fasta):
print trinity_fasta
fixed_mmetsp_ref=fix_fasta_reference(reference_filename,mmetsp_assemblies)
transrate(transrate_reference_dir,sample,trinity_fasta,mmetsp_assemblies_dir,fixed_mmetsp_ref)
transrate_reverse(transrate_reverse_dir,sample,trinity_fasta,mmetsp_assemblies_dir,fixed_mmetsp_ref)
else:
print "Trinity failed:",newdir
trinity_fail.append(newdir)
transrate_assemblies_ref=transrate_reference_dir+sample+"/assemblies.csv"
transrate_reverse_assemblies=transrate_reverse_dir+sample+"/assemblies.csv"
print transrate_assemblies_ref
print transrate_reverse_assemblies
if os.path.isfile(transrate_assemblies_ref):
data1=parse_transrate_stats(transrate_assemblies_ref)
data_frame1=build_DataFrame(data_frame1,data1)
if os.path.isfile(transrate_reverse_assemblies):
data2=parse_transrate_stats(transrate_reverse_assemblies)
data_frame2=build_DataFrame(data_frame2,data2)
print "This is the number of times Trinity failed:"
print len(trinity_fail)
print trinity_fail
return data_frame1,data_frame2
def get_assemblies_data(data_frame,transrate_dir):
listofdirs=os.listdir(transrate_dir)
for dirname in listofdirs:
transrate_assemblies=transrate_dir+dirname+"/assemblies.csv"
print transrate_assemblies
if os.path.isfile(transrate_assemblies):
data=parse_transrate_stats(transrate_assemblies)
data_frame=build_DataFrame(data_frame,data)
else:
print "File missing:",transrate_assemblies
return data_frame
def get_ref_transrate(transrate_dir):
listdirs=os.listdir(transrate_dir)
print listdirs
for dirname in listdirs:
newdir=transrate_dir+dirname+"/"
print newdir
newfile=newdir+"assemblies.csv"
if os.path.isfile(newfile):
print "Exists:",newfile
else:
print "Does not exist:",newfile
basedir = "/mnt/scratch/ljcohen/mmetsp/"
mmetsp_assemblies_dir = "/mnt/research/ged/lisa/mmetsp/imicrobe/cds/"
datafiles=["MMETSP_SRA_Run_Info_subset_msu1.csv","MMETSP_SRA_Run_Info_subset_msu2.csv","MMETSP_SRA_Run_Info_subset_msu3.csv","MMETSP_SRA_Run_Info_subset_msu4.csv",
"MMETSP_SRA_Run_Info_subset_msu5.csv","MMETSP_SRA_Run_Info_subset_msu6.csv","MMETSP_SRA_Run_Info_subset_msu7.csv"]
data_frame1=pd.DataFrame()
data_frame2=pd.DataFrame()
for datafile in datafiles:
url_data=get_data(datafile)
print url_data
data_frame1,data_frame2=execute(data_frame1,data_frame2,url_data,basedir,mmetsp_assemblies_dir)
data_frame1.to_csv("transrate_reference_scores_cds.csv")
data_frame2.to_csv("transrate_reverse_scores_cds.csv")