Add VF tabular comparison views.

docs/CHANGELOG.md

@@ -17,6 +17,7 @@ to [Common Changelog](https://common-changelog.org)
 
 ### Added
 
+- Add VF tabular comparison views. ([#58](https://github.com/metagenlab/zDB/pull/58)) (Niklaus Johner)
 - Add VF Venn diagram view. ([#58](https://github.com/metagenlab/zDB/pull/58)) (Niklaus Johner)
 - Add VF hit extraction view. ([#58](https://github.com/metagenlab/zDB/pull/58)) (Niklaus Johner)
 - Add VF comparison index view and link it in the menu and home page. ([#58](https://github.com/metagenlab/zDB/pull/58)) (Niklaus Johner)

webapp/chlamdb/forms.py

@@ -112,7 +112,7 @@ def get_genomes(self):
     return PlotForm
 
 
-def make_metabo_from(db, add_box=False, add_amr_choices=False):
+def make_metabo_from(db, add_box=False, type_choices=None):
 
     accession_choices, rev_index = get_accessions(db)
 
@@ -132,11 +132,9 @@ class MetaboForm(forms.Form):
             input_box = forms.CharField(
                 widget=forms.Textarea(attrs={'cols': 10, 'rows': 10}))
 
-        if add_amr_choices:
+        if type_choices:
             comp_type = forms.ChoiceField(
-                choices=(("gene", "Gene"),
-                         ("class", "Class"),
-                         ("subclass", "Subclass")),
+                choices=type_choices,
                 required=True
             )
 
@@ -149,7 +147,7 @@ def __init__(self, *args, **kwargs):
             rows = [Row('targets')]
             if add_box:
                 rows.append(Row('input_box'))
-            if add_amr_choices:
+            if type_choices:
                 rows.append(Row('comp_type'))
 
             self.helper.layout = Layout(

webapp/chlamdb/urls.py

@@ -9,6 +9,7 @@
 
 
 urlpatterns = [
+    re_path(r'^vf_comparison', tabular_comparison.VfComparisonView.as_view(), name="vf_comparison"),  # noqa
     re_path(r'^venn_vf/$', venn.VennVfView.as_view(), name="venn_vf"),
     re_path(r'^venn_pfam/$', venn.VennPfamView.as_view(), name="venn_pfam"),
     re_path(r'^venn_orthogroup/$', venn.VennOrthogroupView.as_view(), name="venn_orthogroup"),  # noqa

webapp/lib/queries.py

@@ -26,6 +26,28 @@ def gen_where_clause(self, search_on, entries):
             raise RuntimeError(f"Searching on {search_on} is not supported")
         return where_clause
 
+    def get_hits(self, taxids):
+        where_clause = self.gen_where_clause("taxid", taxids)
+        columns = ["bioentry.taxon_id",
+                   f"{self.hit_table}.{self.id_col}",
+                   "evalue",
+                   "prot_name",
+                   "vfid",
+                   "category",
+                   ]
+        query = (
+            f"SELECT {', '.join(columns)} "
+            f"FROM {self.hit_table} "
+            f"INNER JOIN {self.decription_table} ON {self.decription_table}.{self.id_col} = {self.hit_table}.{self.id_col} "
+            f"INNER JOIN sequence_hash_dictionnary AS hsh ON hsh.hsh = {self.hit_table}.hsh "
+            "INNER JOIN seqfeature ON hsh.seqid = seqfeature.seqfeature_id "
+            "INNER JOIN bioentry ON seqfeature.bioentry_id = bioentry.bioentry_id "
+            f"WHERE {where_clause} "
+        )
+        results = self.server.adaptor.execute_and_fetchall(query, taxids)
+        df = self.to_pandas_frame(results, [col.split(".")[-1] for col in columns])
+        return df
+
     def get_hit_counts(self, ids, indexing="taxid", search_on="taxid",
                        keep_taxid=False, plasmids=None):
         if indexing == "seqid":

webapp/views/mixins.py

@@ -254,6 +254,10 @@ class VfViewMixin(BaseViewMixin):
     def get_hit_counts(self):
         return self.db.vf.get_hit_counts
 
+    @property
+    def get_hits(self):
+        return self.db.vf.get_hits
+
     def get_hit_descriptions(self, ids, transformed=True):
         descriptions = self.db.vf.get_hit_descriptions(ids)
         descriptions = descriptions.set_index("vf_gene_id", drop=False)

webapp/views/tabular_comparison.py

@@ -3,7 +3,7 @@
 from django.views import View
 
 from views.mixins import (AmrViewMixin, CogViewMixin, KoViewMixin,
-                          OrthogroupViewMixin, PfamViewMixin)
+                          OrthogroupViewMixin, PfamViewMixin, VfViewMixin)
 from views.utils import (format_cog, format_ko, format_lst_to_html,
                          format_orthogroup, my_locals)
 
@@ -13,6 +13,7 @@ class TabularComparisonViewBase(View):
     template = 'chlamdb/tabular_comparison.html'
     hist_colour_index_shift = 0
     tab_name = "comp"
+    table_headers = None
 
     def dispatch(self, request, *args, **kwargs):
         self.comp_metabo_form = self.make_metabo_from()
@@ -111,6 +112,11 @@ def form_help(self):
     def first_coloured_row(self):
         return len(self.base_info_headers)
 
+    @property
+    def base_info_headers(self):
+        return [self.colname_to_header(colname)
+                for colname in self.base_info_accessors]
+
 
 class PfamComparisonView(TabularComparisonViewBase, PfamViewMixin):
 
@@ -125,11 +131,6 @@ class PfamComparisonView(TabularComparisonViewBase, PfamViewMixin):
     corresponding Pfam entry.
     """
 
-    @property
-    def base_info_headers(self):
-        return [self.colname_to_header(colname)
-                for colname in self.base_info_accessors]
-
     def get_table_rows(self):
         pfam_hits = self.get_hit_counts(ids=self.targets)
         pfam_defs = self.get_hit_descriptions(pfam_hits.index.tolist(),
@@ -280,8 +281,12 @@ class AmrComparisonView(TabularComparisonViewBase, AmrViewMixin):
     "plus" proteins are included with a less stringent criteria.<br>
     """
 
+    type_choices = (("gene", "Gene"),
+                    ("class", "Class"),
+                    ("subclass", "Subclass"))
+
     def make_metabo_from(self):
-        return make_metabo_from(self.db, add_amr_choices=True)
+        return make_metabo_from(self.db, type_choices=self.type_choices)
 
     @property
     def base_info_accessors(self):
@@ -292,11 +297,6 @@ def base_info_accessors(self):
         elif self.comp_type == "class":
             return ["Class"]
 
-    @property
-    def base_info_headers(self):
-        return [self.colname_to_header(colname)
-                for colname in self.base_info_accessors]
-
     @property
     def table_help(self):
         if self.comp_type == "gene":
@@ -326,3 +326,53 @@ def get_table_rows(self):
     @property
     def hist_colour_index_shift(self):
         return len(self.targets)
+
+
+class VfComparisonView(TabularComparisonViewBase, VfViewMixin):
+
+    _table_help = """
+    The ouput table contains the number of times a given {} appears
+    in the selected genomes, color coded according to the e-value
+    of the best hit for that genome.<br>
+    <br> Counts can be reordrered by clicking on column headers.<br>
+    """
+
+    type_choices = (("vf_gene_id", "VF Gene"),
+                    ("vfid", "VF"),
+                    ("category", "VF Category"))
+
+    def make_metabo_from(self):
+        return make_metabo_from(self.db, type_choices=self.type_choices)
+
+    @property
+    def base_info_accessors(self):
+        if self.comp_type == "vf_gene_id":
+            return ["vf_gene_id", "prot_name", "vfid", "category"]
+        elif self.comp_type == "vfid":
+            return ["vfid", "category"]
+        elif self.comp_type == "category":
+            return ["category"]
+
+    @property
+    def table_help(self):
+        return self._table_help.format(self.comp_type)
+
+    def get_table_rows(self):
+        hits = self.get_hits(self.targets)
+        hits = hits.where(hits.notna(), "-")
+        table_rows = []
+        for groupid, data in hits.groupby(self.comp_type):
+            row = data.iloc[0][self.base_info_accessors].tolist()
+            taxonids = data["taxon_id"]
+            values = [len(taxonids[taxonids == target_id])
+                      for target_id in self.targets]
+            colours = [data[taxonids == target_id]["evalue"].max() if value
+                       else 0 for value, target_id in zip(values, self.targets)]
+            row.extend(values)
+            row.extend(colours)
+            table_rows.append(row)
+        return table_rows
+
+    @property
+    def hist_colour_index_shift(self):
+        return len(self.targets)

webapp/views/utils.py

@@ -31,7 +31,7 @@ def safe_replace(string, search_string, replace_string):
         'orthogroup_comparison', 'pan_genome_orthogroup', 'plot_heatmap_orthogroup',
         'venn_orthogroup'],
     'Comparisons: Virulence Factors': [
-        'entry_list_vf', 'index_comp_vf', 'extract_vf', 'venn_vf'],
+        'entry_list_vf', 'index_comp_vf', 'extract_vf', 'venn_vf', 'vf_comparison'],
     'Genome alignments: Circos plot': ['circos'],
     'Genome alignments: Plot region': ['plot_region'],
     'Genomes: table of contents': ['extract_contigs', 'genomes_intro'],