Merge pull request #15 from stephenshank/master

Scrolling, BAM, SVG

.gitignore

@@ -10,3 +10,4 @@ dist/alignment.js
 *.svg
 *.ttf
 *.eot
+tags*

README.md

@@ -43,3 +43,22 @@ Start the development server:
 ```
 yarn start
 ```
+
+Visit `localhost:8000` in a browser (will read from environment variable `$PORT`).
+
+Note that this starts `webpack` in watch mode; refresh to observe changes.
+
+## Deployment
+
+### Application
+
+```
+yarn build-app
+yarn serve
+```
+
+### Library
+
+```
+yarn build-lib
+```

dist/data/H3trunk.new

@@ -0,0 +1 @@
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dist/data/Simple.fasta

@@ -1,9 +1,6 @@
 >Seq1
-ATCGTA
-ATTGCA
+ATCGTAATTGCA
 >Seq2
-CTCGTA
-ATGGCC
+CTCGTAATGGCC
 >Seq3
-GTCGTC
-AATGCT
+GTCGTCAATGCT

extract_genbank_information.py

@@ -0,0 +1,78 @@
+import sys
+import json
+import argparse
+from itertools import chain
+
+try:
+    from Bio import SeqIO
+except ImportError:
+    print('BioPython not installed!')
+    print('Please visit https://biopython.org/wiki/Download for instructions.')
+    sys.exit(1)
+
+
+parser = argparse.ArgumentParser(
+    description='Write GenBank information to a JSON file for alignment.js.'
+)
+
+parser.add_argument(
+    '-i', '--input',
+    metavar='INPUT',
+    type=str,
+    help='Input GenBank file',
+    required=True
+)
+
+parser.add_argument(
+    '-o', '--output',
+    metavar='OUTPUT',
+    type=str,
+    help='Output JSON file',
+    required=True
+)
+
+
+args = parser.parse_args()
+
+
+def extract_site_information(feature):
+    return list(chain(*[
+        [
+            {
+                'name': feature.qualifiers['site_type'][0],
+                'site': site,
+                'type': 'site'
+            }
+            for site in part
+        ]
+        for part in feature.location.parts
+    ]))
+
+
+def extract_region_information(feature):
+    return {
+        'name': feature.qualifiers['region_name'][0],
+        'start': int(feature.location.start),
+        'end': int(feature.location.end),
+        'type': 'region'
+    }
+
+
+def extract_functional_information(features):
+    all_information = []
+    for feature in features:
+          if feature.type == 'Site':
+              result = extract_site_information(feature)
+              all_information.append(result)
+          elif feature.type == 'Region':
+              result = extract_region_information(feature)
+              all_information.append([result])
+    return sum(all_information, [])
+
+
+record = next(SeqIO.parse(args.input, 'genbank'))
+information = extract_functional_information(record.features)
+
+with open(args.output, 'w') as json_file:
+    json.dump(information, json_file, indent=2)
+