diff --git a/scripts/odp b/scripts/odp index 847b01a..35e8255 100644 --- a/scripts/odp +++ b/scripts/odp @@ -207,16 +207,16 @@ if "plot_LGs" not in config: config["plot_LGs"] = True if config["plot_LGs"]: - ## This set of files plots the installed LGs against all of the datasets - #file_targets += [config["tool"] + "/step0-blastp_results/{}_against_{}.hmmsearch.filt.blastp".format(hmm, sp) - # for sp in config["analysisspecies"] for hmm in config["prot_to_color"]] - ## color by the things in the chrom settings - #file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_xy_reciprocal_best_hits.coloredby_{}.plotted.rbh".format(y, x, y) - # for x in config["analysispairs"] for y in config["prot_to_color"]] - #file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_xy_synteny_coloredby_{}.pdf".format(y, x, y) - # for x in config["analysispairs"] for y in config["prot_to_color"]] - #file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_yx_synteny_coloredby_{}.pdf".format(y, x, y) - # for x in config["analysispairs"] for y in config["prot_to_color"]] + # This set of files plots the installed LGs against all of the datasets + file_targets += [config["tool"] + "/step0-blastp_results/{}_against_{}.hmmsearch.filt.blastp".format(hmm, sp) + for sp in config["analysisspecies"] for hmm in config["prot_to_color"]] + # color by the things in the chrom settings + file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_xy_reciprocal_best_hits.coloredby_{}.plotted.rbh".format(y, x, y) + for x in config["analysispairs"] for y in config["prot_to_color"]] + file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_xy_synteny_coloredby_{}.pdf".format(y, x, y) + for x in config["analysispairs"] for y in config["prot_to_color"]] + file_targets += [config["tool"] + "/step2-figures/synteny_coloredby_{}/{}_yx_synteny_coloredby_{}.pdf".format(y, x, y) + for x in config["analysispairs"] for y in config["prot_to_color"]] # We also want to plot the ALGs as if they were genomes, against the individual species # This line specifically is for testing the RBH-as-a-species analysis