add region method to parse region id

fix compat module imports

chanjo/cli/calculate.py

@@ -39,13 +39,17 @@ def gene(context, gene_ids):
 @click.option('-p', '--per', type=click.Choice(['exon', 'sample']),
               help='report stats per sample/exon')
 @click.argument('chromosome', type=str)
-@click.argument('start', type=int)
-@click.argument('end', type=int)
+@click.argument('start', type=int, required=False)
+@click.argument('end', type=int, required=False)
 @click.pass_context
 def region(context, sample, per, chromosome, start, end):
     """Report mean statistics for a region of exons."""
-    results = context.parent.api.region(chromosome, start, end,
-                                        sample_id=sample, per=per)
+    api = context.parent.api
+    if start is None:
+        logger.debug('region id detected, parse string')
+        results = api.region_alt(chromosome, sample_id=sample, per=per)
+    else:
+        results = api.region(chromosome, start, end, sample_id=sample, per=per)
     if per == 'exon':
         dump_json(*results)
     else:

chanjo/store/api.py

@@ -4,7 +4,7 @@
 
 from sqlalchemy.sql import func
 
-from chanjo._compat import itervalues
+from chanjo.compat import itervalues
 from .core import Store
 from .models import Exon, ExonStatistic, Gene, Sample, Transcript
 from .utils import group_by_field, predict_gender
@@ -107,6 +107,23 @@ def mean(self, *samples):
         sample_groups = group_by_field(results, name='sample_id')
         return sample_groups
 
+    def region_alt(self, region_id, sample_id=None, per=None):
+        """Parse region id as input for `region` method.
+
+        Args:
+            region_id (str): for example 1:1242314-1243419
+            sample_id (Optional[str]): filter to only a single sample
+            per (Optional[str]): report on a per exon basis ("exon")
+
+        Returns:
+            dict: weighted metrics (across samples)
+        """
+        chromosome, pos_str = region_id.split(':')
+        start, end = [int(pos) for pos in pos_str.split('-')]
+        data = self.region(chromosome, start, end, sample_id=sample_id,
+                           per=per)
+        return data
+
     def region(self, chromosome, start, end, sample_id=None, per=None):
         """Report coverage across a genomics region (of exons).
 
@@ -262,7 +279,7 @@ def incomplete_exons(self, level=10, threshold=100, group_id=None,
         return query
 
     def gene_panel(self, gene_ids, group_id=None, sample_ids=None):
-        """Report metrics for a panel of genes.
+        """Report mean coverage (+ completeness) for a panel of genes.
 
         Args:
             gene_ids (List[str]): gene ids for the panel

chanjo/store/utils.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from chanjo._compat import itervalues
+from chanjo.compat import itervalues
 
 
 def group_by_field(results, name='field_id'):