def dinuc_shuffling_generator(argu):
seqs, fg_gc_list, fg_lengths = get_seqs(argu.fg_file)
bg_gc_list, bg_lengths = dinuc_shuff.generate_sequences(seqs, argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Generated background", "GC", "\nGC plot")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Generated background", "Len", "\nLength plot")
def dinuc_shuffling_generator(argu):
seqs, fg_gc_list, fg_lengths = get_seqs(argu.fg_file)
bg_gc_list, bg_lengths = dinuc_shuff.generate_sequences(seqs, argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Generated background", "GC", "\nGC plot")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Generated background", "Len", "\nLength plot")
def gc_compo_len_generator(argu):
fg_gc_list, fg_gc_bins, fg_lengths = GC_compo.fg_len_GC_bins(argu.fg_file)
bg_gc_list, bg_gc_bins, bg_lengths = GC_compo.bg_len_GC_bins(argu.bg_file)
match_gc_list, match_lengths = GC_compo.generate_len_sequences(
fg_gc_bins, bg_gc_bins, argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground", "Background",
"GCbefore", "\nGC plot before")
make_r_gc_plots(fg_gc_list, match_gc_list, "Foreground",
"Matching Background", "GCafter", "GC plot after")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground", "Backgronud",
"Lenbefore", "\nLength plot before")
make_r_len_plots(fg_lengths, match_lengths, "Foreground",
"Matching Background", "Lenafter", "Length plot after")
def gc_compo_len_generator(argu):
fg_gc_list, fg_gc_bins, fg_lengths = GC_compo.fg_len_GC_bins(argu.fg_file)
bg_gc_list, bg_gc_bins, bg_lengths = GC_compo.bg_len_GC_bins(argu.bg_file)
match_gc_list, match_lengths = GC_compo.generate_len_sequences(fg_gc_bins,
bg_gc_bins,
argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Background", "GCbefore", "\nGC plot before")
make_r_gc_plots(fg_gc_list, match_gc_list, "Foreground",
"Matching Background", "GCafter", "GC plot after")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Backgronud", "Lenbefore", "\nLength plot before")
make_r_len_plots(fg_lengths, match_lengths, "Foreground",
"Matching Background", "Lenafter", "Length plot after")
def gc_compo_window_generator_no_len(argu):
fg_gc_list, fg_gc_bins, fg_lengths = GC_window_compo.fg_GC_bins(
argu.fg_file, argu.winlen, argu.step)
bg_gc_list, bg_gc_bins, bg_lengths = GC_window_compo.bg_GC_bins(
argu.bg_file)
match_gc_list, match_lengths = GC_window_compo.generate_sequences(
fg_gc_bins, bg_gc_bins, argu.deviation, argu.winlen, argu.step,
argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground",
"Background", "GCbefore", "\nGC plot before")
make_r_gc_plots(fg_gc_list, match_gc_list, "Foreground",
"Matching Backgronud", "GCafter", "GC plot after")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground",
"Backgronud", "Lenbefore", "\nLength plot before")
make_r_len_plots(fg_lengths, match_lengths, "Foreground",
"Matching Backgronud", "Lenafter", "Length plot after")
def gc_compo_window_generator_no_len(argu):
fg_gc_list, fg_gc_bins, fg_lengths = GC_window_compo.fg_GC_bins(
argu.fg_file, argu.winlen, argu.step)
bg_gc_list, bg_gc_bins, bg_lengths = GC_window_compo.bg_GC_bins(
argu.bg_file)
match_gc_list, match_lengths = GC_window_compo.generate_sequences(
fg_gc_bins, bg_gc_bins, argu.deviation, argu.winlen, argu.step,
argu.nfold)
make_r_gc_plots(fg_gc_list, bg_gc_list, "Foreground", "Background",
"GCbefore", "\nGC plot before")
make_r_gc_plots(fg_gc_list, match_gc_list, "Foreground",
"Matching Backgronud", "GCafter", "GC plot after")
make_r_len_plots(fg_lengths, bg_lengths, "Foreground", "Backgronud",
"Lenbefore", "\nLength plot before")
make_r_len_plots(fg_lengths, match_lengths, "Foreground",
"Matching Backgronud", "Lenafter", "Length plot after")