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)
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)
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)
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)
