Esempio n. 1
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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")
Esempio n. 2
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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")
Esempio n. 3
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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")
Esempio n. 4
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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")
Esempio n. 5
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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")
Esempio n. 6
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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")