shifter_gui.py

from Tkinter import *
from tkFileDialog import askopenfilename
import sys, os, shutil

option = ''
dir_list = {}
vcf_files = []
bam_files = []

def make_first_dirs(target_run):
    ''' This function should be rearranged to list dirs to create in a 
        reverse hierarchy the dic.keys() method seems to have no 
        ordering... e.g. BAM-coverage cannot be created before BAM '''
    dir_list["VCF_dir"] = os.path.join(dir_list["base"],target_run+"_VCF")
    os.mkdir(dir_list["VCF_dir"])
    dir_list["VCF_dup"] = os.path.join(dir_list["VCF_dir"], str(target_run)+"_duplicate VCF")
    os.mkdir(dir_list["VCF_dup"])
    dir_list["VCF_run1"] = os.path.join(dir_list["VCF_dir"], "Run 1")
    os.mkdir(dir_list["VCF_run1"])
    dir_list["VCF_run2"] = os.path.join(dir_list["VCF_dir"], "Run 2")
    os.mkdir(dir_list["VCF_run2"])
    dir_list["BAM_dir"] = os.path.join(dir_list["base"],target_run+"_BAM")
    os.mkdir(dir_list["BAM_dir"])
    dir_list["BAM_coverage"] = os.path.join(dir_list["BAM_dir"], str(target_run+" coverage report"))
    os.mkdir(dir_list["BAM_coverage"])
    dir_list["neg_dir"] = os.path.join(dir_list["base"], "negative")
    os.mkdir(dir_list["neg_dir"])

#Bam and Bam.bai (index files) present
def identify_bams(MiSeq_file_list):
    for x in MiSeq_file_list:
        if x[-4:] == ".bam":
            bam_files.append(x)
        elif x[-4:] == ".bai":
            bam_files.append(x)
    move_bams(bam_files)

def move_bams(bam_files):
    dir_list["data"]
    for x in bam_files: 
        shutil.move(os.path.join(dir_list["data"],x), os.path.join(dir_list["BAM_dir"], x))

def identify_vcfs(MiSeq_file_list):
    for x in MiSeq_file_list:
        if x[-4:] == ".vcf":
			if x.split('.')[1] == 'vcf':
				vcf_files.append(x)

#Is file name storage important? 
def identify_patients(vcf_list):
    ''' Identifies each unique D number (keys)'''
    patients = {}
    for x in vcf_list:
        filename_components = x.split('-')
        d_number = str(filename_components[0]) + "." + str(filename_components[1])
        if d_number in patients:
            print 'patient repeat'
        else:   
            #Create a list & append filename
            patients[d_number] = 1
    return patients

def create_patient_folders(patients):
    ''' Uses the keys from the patients dictionary
        (contains the VCF file names) and uses them
        to populate the main run directory with a 
        file for each patient '''
    unique_d_numbers = patients.keys()
    for x in unique_d_numbers:
        os.mkdir(os.path.join(dir_list["base"],x))

def sort_vcfs(vcf_files):
    ''' Should read all VCF file names and sort into
        Run 1 or 2 based on file name 
        At this point no VCF files have been moved '''
    for x in vcf_files:
        file_name_list = x.split("_")
        new_filename = file_name_list[0][0:-2] +'_'+ file_name_list[1]
        if file_name_list[0][-2:] == '-1':
            #move to 1
            shutil.move(os.path.join(dir_list["data"], x), os.path.join(dir_list["VCF_run1"], new_filename))
        elif file_name_list[0][-2:] == '-2':
            #move to 2
            shutil.move(os.path.join(dir_list["data"], x), os.path.join(dir_list["VCF_run2"], new_filename))

def run_shifter(run_number):
    dir_list["base"] = os.path.join(os.getcwd(), run_number)
    MiSeq_file = os.listdir(dir_list["base"])[0]
    #Hard coded, but consistency from MiSeq output
    dir_list["data"] = os.path.join(dir_list["base"], MiSeq_file, "Data",     "Intensities", "Basecalls", "Alignment")
    MiSeq_file_list = os.listdir(dir_list["data"])
    make_first_dirs(run_number)
    identify_bams(MiSeq_file_list)
    identify_vcfs(MiSeq_file_list)
    patients = identify_patients(vcf_files)
    create_patient_folders(patients)
    sort_vcfs(vcf_files)

def open_file():
    name = askopenfilename()
    #Add name to entry free text
    entry.insert(0, name)
    print name

def About():
    #fill this
    print "This is a simple example of a menu"
    #Operating instructions

def run_parser():
    run_number = entry.get()
    run_shifter(run_number)
    root.quit()
    
root = Tk()
menu = Menu(root)
root.config(menu=menu)
helpmenu = Menu(menu)
menu.add_command(label="Help", command=About)

text_in_label = Label(root, text="Run Number:")
text_in_label.grid(row=0, column=1, sticky = 'w')
entry = Entry(root)
entry.grid(row=0,column=2, sticky = 'w')
button = Button(root, text="Browse...", command=open_file)
button.grid(row=0, column=3)


button = Button(root, text="QUIT", fg="red", command=root.quit)
button.grid(row=3, column=1)
parser= Button(root, text="Sort", fg="blue", command=run_parser)
parser.grid(row=3, column=2)

mainloop()