Commit 552e35de authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Report : deal with non found sections

parent 8f2897b3
......@@ -57,10 +57,14 @@ def gather_outputs():
# Get alpha group significance data
if os.path.isfile(INDIR + "/alpha_group_significance/shannon-group-significance/index.html"):
shutil.copytree(INDIR + "/alpha_group_significance/shannon-group-significance", REPORT_DIR + "/diversity/alpha_group_significance/shannon-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/evenness-group-significance", REPORT_DIR + "/diversity/alpha_group_significance/evenness-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/faith_pd-group-significance", REPORT_DIR + "/diversity/alpha_group_significance/faith_pd-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/observed_otus-group-significance", REPORT_DIR + "/diversity/alpha_group_significance/observed_otus-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/shannon-group-significance", REPORT_DIR +
"/diversity/alpha_group_significance/shannon-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/evenness-group-significance", REPORT_DIR +
"/diversity/alpha_group_significance/evenness-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/faith_pd-group-significance", REPORT_DIR +
"/diversity/alpha_group_significance/faith_pd-group-significance")
shutil.copytree(INDIR + "/alpha_group_significance/observed_otus-group-significance",
REPORT_DIR + "/diversity/alpha_group_significance/observed_otus-group-significance")
template_data["alpha_shannon"] = "diversity/alpha_group_significance/shannon-group-significance/index.html"
template_data["alpha_eveness"] = "diversity/alpha_group_significance/evenness-group-significance/index.html"
template_data["alpha_faith"] = "diversity/alpha_group_significance/faith_pd-group-significance/index.html"
......@@ -68,15 +72,34 @@ def gather_outputs():
# Get beta group significance data
if os.path.isfile(INDIR + "/beta_group_significance/bray_curtis_distance_matrix/index.html"):
shutil.copytree(INDIR + "/beta_group_significance/bray_curtis_distance_matrix", REPORT_DIR + "/diversity/beta_group_significance/bray_curtis_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/jaccard_distance_matrix", REPORT_DIR + "/diversity/beta_group_significance/jaccard_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/unweighted_unifrac_distance_matrix", REPORT_DIR + "/diversity/beta_group_significance/unweighted_unifrac_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/weighted_unifrac_distance_matrix", REPORT_DIR + "/diversity/beta_group_significance/weighted_unifrac_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/bray_curtis_distance_matrix", REPORT_DIR +
"/diversity/beta_group_significance/bray_curtis_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/jaccard_distance_matrix", REPORT_DIR +
"/diversity/beta_group_significance/jaccard_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/unweighted_unifrac_distance_matrix",
REPORT_DIR + "/diversity/beta_group_significance/unweighted_unifrac_distance_matrix")
shutil.copytree(INDIR + "/beta_group_significance/weighted_unifrac_distance_matrix",
REPORT_DIR + "/diversity/beta_group_significance/weighted_unifrac_distance_matrix")
template_data["bray_curtis"] = "diversity/beta_group_significance/bray_curtis_distance_matrix/index.html"
template_data["jaccard"] = "diversity/beta_group_significance/jaccard_distance_matrix/index.html"
template_data["uw_unifrac"] = "diversity/beta_group_significance/unweighted_unifrac_distance_matrix/index.html"
template_data["w_unifrac"] = "diversity/beta_group_significance/weighted_unifrac_distance_matrix/index.html"
# Get ADONIS
if os.path.isfile(INDIR + "/adonis/bray_curtis_distance_matrix/index.html"):
shutil.copytree(INDIR + "/adonis/bray_curtis_distance_matrix", REPORT_DIR +
"/diversity/adonis/bray_curtis_distance_matrix")
shutil.copytree(INDIR + "/adonis/jaccard_distance_matrix", REPORT_DIR +
"/diversity/adonis/jaccard_distance_matrix")
shutil.copytree(INDIR + "/adonis/unweighted_unifrac_distance_matrix",
REPORT_DIR + "/diversity/adonis/unweighted_unifrac_distance_matrix")
shutil.copytree(INDIR + "/adonis/weighted_unifrac_distance_matrix",
REPORT_DIR + "/diversity/adonis/weighted_unifrac_distance_matrix")
template_data["bray_curtis_adonis"] = "diversity/adonis/bray_curtis_distance_matrix/index.html"
template_data["jaccard_adonis"] = "diversity/adonis/jaccard_distance_matrix/index.html"
template_data["uw_unifrac_adonis"] = "diversity/adonis/unweighted_unifrac_distance_matrix/index.html"
template_data["w_unifrac_adonis"] = "diversity/adonis/weighted_unifrac_distance_matrix/index.html"
# Get taxonomic composition
if os.path.isfile(INDIR + "/taxonomy/barplot/index.html"):
shutil.copytree(INDIR + "/taxonomy/barplot", REPORT_DIR + "/taxonomy/barplot")
......@@ -84,11 +107,16 @@ def gather_outputs():
template_data["taxo_barplot"] = "taxonomy/barplot/index.html"
template_data["taxo_taxons"] = "taxonomy/taxons/index.html"
# Get Differential abundance
# Get Differential abundance ANCOM
if os.path.isfile(INDIR + "/ancom/volcano/index.html"):
shutil.copytree(INDIR + "/ancom/volcano", REPORT_DIR + "/ancom/volcano")
template_data["ancom_volcano"] = "ancom/volcano/index.html"
# Get Differential abundance DESeq2
if os.path.isdir(INDIR + "/deseq2"):
shutil.copytree(INDIR + "/deseq2", REPORT_DIR + "/deseq2")
template_data["deseq2"] = "deseq2"
# Get Phylogenetic tree
if os.path.isfile(INDIR + "/phylogenetic_tree/tree.nwk"):
os.mkdir(REPORT_DIR + "/phylogenetic_tree")
......
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