Create script to draw html graph to visualize STR results

plot/high_normal_range_by_patho.csv

+Gene;High normal range
+AFF2;39
+AR;35
+ATN1;34
+ATXN1;38
+ATXN10;20
+ATXN2;24
+ATXN3;36
+ATXN7;35
+ATXN8OS;34
+C9ORF72;19
+CACNA1A;7
+CNBP;26
+CSTB;3
+DIP2B;NA
+DMPK;37
+FMR1;45
+FXN;32
+HTT;34
+JPH3;27
+NOP56;8
+PHOX2B;20
+PPP2R2B;45
+TBP;42
+TCF4;NA
+BEAN/TK2;NA
+DAB1;NA
+SAMD12;NA
\ No newline at end of file

plot/launch_triplets_plotly.sh

+#! /bin/sh
+
+SCRIPT="$(dirname "$(readlink -f "$0")")/triplets_plotly.py"
+
+cd '/work/gad/shared/analyse/STR/results2020-01-09' || exit 1
+for locus_tsv in *.tsv; do
+    locus="$(basename "$locus_tsv" ".tsv")"
+    echo "Processing $locus" >&2
+    "$SCRIPT" "$locus" > "$locus.html"
+done
+

plot/triplets_plotly.py

+#! /usr/bin/env python3
+
+### ASDP PIPELINE ###
+## triplets_plotly.py
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to get automatically graphics from expansion pipeline results from getResults.py with Plotly
+## Usage :
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20200202
+## last revision date : 20200202
+## Known bugs : None
+
+import collections
+import csv
+import os
+import sys
+
+path = '/work/gad/shared/analyse/STR/results2020-01-09'
+
+def display_console_graph(title, data):
+    print(title)
+    for x, y in data:
+        print(f'{x}\t{"*" * y}')
+
+def display_html_graph(title, data):
+    import plotly.graph_objects as go
+
+    fig = go.Figure(
+        data=[go.Bar(
+            x=[x for (x, y) in data],
+            y=[y for (x, y) in data]
+        )],
+        layout_title_text=title
+    )
+
+    print(fig.to_html())
+
+def graph_locus(locus):
+    title = f'Effectif pour chaque nombre de répétitions au locus {locus}'
+    with open(f'{path}{os.sep}{locus}.tsv') as result_file:
+        tsvreader = csv.reader(result_file, delimiter='\t')
+        try:
+            next(tsvreader)
+            counter = collections.Counter()
+            counter[0] = 0
+            for row in tsvreader:
+                if row[1] not in ['.', 'nofile']:
+                    for count in row[1].split(','):
+                        counter[int(count)] += 1
+        except StopIteration:
+            print('Input file is empty', file=sys.stderr)
+            sys.exit(1)
+        data = sorted(counter.items())
+        #display_console_graph(title, data)
+        display_html_graph(title, data)
+
+if __name__ == '__main__':
+    if len(sys.argv) != 2:
+        print(f'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS>', file=sys.stderr)
+        sys.exit(1)
+    graph_locus(sys.argv[1])