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combine.py
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combine.py
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# combines files from same sample
# first 9 fields must be the same for F. heteroclitus
# first 8 fields must b the same for all other species
import os
import os.path
import subprocess
from subprocess import Popen,PIPE
import glob
import gzip
import clusterfunc
#dir1="/home/nreid/rnaseq/rawdata/141212_HS2A/"
#dir2="/home/nreid/rnaseq/rawdata/141203_HS4B/"
#dir3="/home/nreid/rnaseq/rawdata/141126_HS3A/"
def sort_filenames_by_genus_species_treatment(listoffiles,basedir):
files={}
for i in listoffiles:
if i.endswith(".fastq.gz"):
genus_species_sample_read=parse_filename(i)
if genus_species_sample_read in files:
files[genus_species_sample_read].append(i)
else:
files[genus_species_sample_read]=[i]
for species in files.keys():
# filestomergelist=find_files_to_merge(files[species],species)
print species
files[species]=sorted(files[species])
print files[species]
print len(files[species])
return files
def combine_files(files,basedir,combine_dir):
clusterfunc.check_dir(combine_dir)
for species in files.keys():
fields=files[species][0].split("_")
extension=fields[-1]
parsed_extension1=extension.split(".")
parsed_extension2=parsed_extension1[1:]
new_extension=".".join(parsed_extension2)
newfilename=get_newfilename(fields,new_extension)
print species
print files[species]
#print newfilename
newfilename=combine_dir+newfilename
files_string=" ".join(files[species])
combine_string="cat "+files_string+" > "+newfilename
print combine_string
workingdir=os.getcwd()
os.chdir(basedir)
#s=subprocess.Popen(combine_string,shell=True)
#s.wait()
os.chdir(workingdir)
def parse_extension(extension):
parsed_extension1=extension.split(".")
parsed_extension2=parsed_extension1[1:]
filenumber=parsed_extension1[0]
trim=parsed_extension1[1]
new_extension=".".join(parsed_extension2)
return filenumber,trim
def find_files_to_merge(fileslist,species):
filestomergelist=[]
for filename in fileslist:
fields=filename.split("_")
return filestomergelist
def get_newfilename(fields,new_extension):
newfilename1="_".join(fields[0:-1])
newfilename=newfilename1+"_"+new_extension
return newfilename
def parse_filename(fastq_filename):
# example filename:
# AWJRDD001_F_similis_BW_1_TCCGCGAA-ATAGAGGC_L002_R1_001.fastq.gz
# 0=flowcell#
# 1=Genus
# 2=spcies
# 3=treatment
# 4=sample#
# 5=barcode
# 6=lane
# 7=read
## this can be parsed by .split(".")
# 8=file#.fastq.gz
# F. heteroclitus:
# AWJRDD002_F_heteroclitus_MDPL_transfer_2_ATTCAGAA-ATAGAGGC_L004_R1_002.fastq.gz
# 0=flowcell#
# 1=Genus
# 2=species
# 3=population
# 4=treatment
# 5=sample#
# 6=barcode
# 7=lane
# 8=read
## this can be parsed by .split(".")
# 9=file#.fastq.gz
listoffilestomerge=[]
fields=fastq_filename.split("_")
flowcell=fields[0]
genus=fields[1]
species=fields[2]
genus_species=genus+"_"+species
if species=="heteroclitus":
population=fields[3]
treatment=fields[4]
sample=fields[5]
barcode=fields[6]
lane=fields[7]
read=fields[8]
extension=fields[9]
filenumber,trim=parse_extension(extension)
genus_species_sample_read=(genus,species,population,treatment,sample,flowcell,lane,read,trim)
return genus_species_sample_read
else:
treatment=fields[3]
sample=fields[4]
barcode=fields[5]
lane=fields[6]
read=fields[7]
extension=fields[8]
filenumber,trim=parse_extension(extension)
population="NA"
genus_species_sample_read=(genus,species,population,treatment,sample,flowcell,lane,read,trim)
return genus_species_sample_read
# how to figure out which files need to be combined?
# the last field will be different
# all the rest of the fields will be the same
# need to collect this information somehow for all files
# put all files to be merged in a list:
#basedir="/home/ljcohen/osmotic_trim/Ph30/"
basedir="/home/ljcohen/osmotic_trim/Ph40/"
listoffiles=os.listdir(basedir)
#print listoffiles
files=sort_filenames_by_genus_species_treatment(listoffiles,basedir)
combine_dir="/home/ljcohen/osmotic_trim/Ph40/combined/"
combine_files(files,basedir,combinedir)