Exemple #1
0
def hardcode():
	SI 	= True
	if SI: #single isoform genes that overlap a single FStitch call
		#===================
		#union of forward and reverse strand FStitch calls
		#BELOW is hardcoding
		#====================
		#FILES
		root 			= "/Users/joeyazo/Desktop/Lab/gro_seq_files"
		refseqFILE 		= root+"/RefSeqHG19.txt"
		FS_forward		= root+"/HCT116/FStitch/DMSO2_3.sorted.fiveprime.pos_segs_IGV.bed"
		FS_reverse  	= root+"/HCT116/FStitch/DMSO2_3.sorted.fiveprime.neg_segs_IGV.bed"
		forward_file_bg = root+"/HCT116/bed_graph_files/DMSO2_3.pos.BedGraph"
		reverse_file_bg = root+"/HCT116/bed_graph_files/DMSO2_3.neg.BedGraph"
		write_out 		= root+"/HCT116/FStitch/single_isoform_FStitch.tsv"
		#====================
		#====================
		#INPUT PARAMETERS
		bins 	= 300

		
		RF 		= load.gene_annotations(refseqFILE)
		FS 		= load.FStitch_annotations(FS_forward, FS_reverse, merge=True)
		filtered= load.filter_single_overlaps(FS, RF)
		load.bedGraphFile(forward_file_bg, reverse_file_bg, 
			filtered, SHOW=False, test=False,
			write_out=write_out)
Exemple #2
0
def hardcode():
    SI = True
    if SI:  #single isoform genes that overlap a single FStitch call
        #===================
        #union of forward and reverse strand FStitch calls
        #BELOW is hardcoding
        #====================
        #FILES
        root = "/Users/joeyazo/Desktop/Lab/gro_seq_files"
        refseqFILE = root + "/RefSeqHG19.txt"
        FS_forward = root + "/HCT116/FStitch/DMSO2_3.sorted.fiveprime.pos_segs_IGV.bed"
        FS_reverse = root + "/HCT116/FStitch/DMSO2_3.sorted.fiveprime.neg_segs_IGV.bed"
        forward_file_bg = root + "/HCT116/bed_graph_files/DMSO2_3.pos.BedGraph"
        reverse_file_bg = root + "/HCT116/bed_graph_files/DMSO2_3.neg.BedGraph"
        write_out = root + "/HCT116/FStitch/single_isoform_FStitch.tsv"
        #====================
        #====================
        #INPUT PARAMETERS
        bins = 300

        RF = load.gene_annotations(refseqFILE)
        FS = load.FStitch_annotations(FS_forward, FS_reverse, merge=True)
        filtered = load.filter_single_overlaps(FS, RF)
        load.bedGraphFile(forward_file_bg,
                          reverse_file_bg,
                          filtered,
                          SHOW=False,
                          test=False,
                          write_out=write_out)
Exemple #3
0
def run(argv):
	
	aw 		= parse_argv.run(argv)
	if aw.exit:
		aw.printErrors()
		print "exiting..."
		return False
	if aw.mod == "formatData":
		if aw.mod2=="FStitchSingleIsoform":
			#====================================
			refseqFILE 		= aw.G["-ref"][0]
			FS_forward 		= aw.G["-ffs"][0]
			FS_reverse 		= aw.G["-rfs"][0]
			forward_file_bg = aw.G["-fbg"][0]
			reverse_file_bg = aw.G["-rbg"][0]
			write_out_dir 	= aw.G["-wo"][0]
			pad 			= float(aw.G["-pad"][0])
			#====================================			
			RF 		= load.gene_annotations(refseqFILE)
			FS 		= load.FStitch_annotations(FS_forward, FS_reverse, merge=True)
			filtered= load.filter_single_overlaps(FS, RF)
			load.bedGraphFile(forward_file_bg, reverse_file_bg, 
				filtered, SHOW=False, test=False,
				write_out=write_out_dir)

		elif aw.mod2=="RefSeqOnly":
			print "RefSeq only option not supported yet"
			
		elif aw.mod2=="FStitchMerged":
			FS_forward 		= aw.G["-ffs"][0]
			FS_reverse 		= aw.G["-rfs"][0]
			forward_file_bg = aw.G["-fbg"][0]
			reverse_file_bg = aw.G["-rbg"][0]
			write_out_dir 	= aw.G["-wo"][0]
			pad 			= float(aw.G["-pad"][0])
			FS 				= load.FStitch_annotations(FS_forward, FS_reverse, 
				merge=True, pad=pad)
			load.bedGraphFile(forward_file_bg, reverse_file_bg, 
				FS, SHOW=False, test=False,
				write_out=write_out_dir)
			


	else: #run MODEL! 
		#====================================
		formatted_file 		= aw.G["-i"][0]
		write_out_dir 		= aw.G["-wo"][0]
		max_k 				= int(aw.G["-k"][0])
		rounds 				= int(aw.G["-it"][0])
		bins 				= int(aw.G["-b"][0])
		specific_chromosome = aw.G["-sc"][0]
		bic 				= float(aw.G["-bic"][0])
		standardize 		= float(aw.G["-st"][0])
		convergence_thresh 	= float(aw.G["-mc"][0])
		max_iterations 		= int(aw.G["-mt"][0])
		move_uniform 		= int(aw.G["-mu"][0])
		#====================================
		D 					= load.formatted_file(formatted_file, bins,specific_chromosome)		
		model_across.run(D, bic, rounds, 
			max_k, standardize, convergence_thresh,
			max_iterations,move_uniform, write_out_dir, specific_chromosome)
Exemple #4
0
def run(argv):

    aw = parse_argv.run(argv)
    if aw.exit:
        aw.printErrors()
        print "exiting..."
        return False
    if aw.mod == "formatData":
        if aw.mod2 == "FStitchSingleIsoform":
            #====================================
            refseqFILE = aw.G["-ref"][0]
            FS_forward = aw.G["-ffs"][0]
            FS_reverse = aw.G["-rfs"][0]
            forward_file_bg = aw.G["-fbg"][0]
            reverse_file_bg = aw.G["-rbg"][0]
            write_out_dir = aw.G["-wo"][0]
            pad = float(aw.G["-pad"][0])
            #====================================
            RF = load.gene_annotations(refseqFILE)
            FS = load.FStitch_annotations(FS_forward, FS_reverse, merge=True)
            filtered = load.filter_single_overlaps(FS, RF)
            load.bedGraphFile(forward_file_bg,
                              reverse_file_bg,
                              filtered,
                              SHOW=False,
                              test=False,
                              write_out=write_out_dir)

        elif aw.mod2 == "RefSeqOnly":
            print "RefSeq only option not supported yet"

        elif aw.mod2 == "FStitchMerged":
            FS_forward = aw.G["-ffs"][0]
            FS_reverse = aw.G["-rfs"][0]
            forward_file_bg = aw.G["-fbg"][0]
            reverse_file_bg = aw.G["-rbg"][0]
            write_out_dir = aw.G["-wo"][0]
            pad = float(aw.G["-pad"][0])
            FS = load.FStitch_annotations(FS_forward,
                                          FS_reverse,
                                          merge=True,
                                          pad=pad)
            load.bedGraphFile(forward_file_bg,
                              reverse_file_bg,
                              FS,
                              SHOW=False,
                              test=False,
                              write_out=write_out_dir)

    else:  #run MODEL!
        #====================================
        formatted_file = aw.G["-i"][0]
        write_out_dir = aw.G["-wo"][0]
        max_k = int(aw.G["-k"][0])
        rounds = int(aw.G["-it"][0])
        bins = int(aw.G["-b"][0])
        specific_chromosome = aw.G["-sc"][0]
        bic = float(aw.G["-bic"][0])
        standardize = float(aw.G["-st"][0])
        convergence_thresh = float(aw.G["-mc"][0])
        max_iterations = int(aw.G["-mt"][0])
        move_uniform = int(aw.G["-mu"][0])
        #====================================
        D = load.formatted_file(formatted_file, bins, specific_chromosome)
        model_across.run(D, bic, rounds, max_k, standardize,
                         convergence_thresh, max_iterations, move_uniform,
                         write_out_dir, specific_chromosome)