PR notes

brkpoints/fragile_finder.py

@@ -16,7 +16,7 @@
 
 ####################################################
 # where the local biodata lives on the host system
-BIODATA = os.environ('BIODATA', '/opt/biodata')
+BIODATA = os.environ.get('BIODATA', '/opt/biodata')
 DEFAULT_DB = '/usr/local/share/Blast/db/human_genomic'
 
 
@@ -133,10 +133,11 @@ def remove_duplicates(fragile_list, distance):
             gene = name[1]
         elif name[4] == 'b':
             gene = name[2]
-        if by_chr.get(gene + '_' + site[1]):
-            by_chr[gene + '_' + site[1]].append(site)
+        chr_key = gene + '_' + site[1]
+        if by_chr.get(chr_key):
+            by_chr[chr_key].append(site)
         else:
-            by_chr[gene + '_' + site[1]] = [site]
+            by_chr[chr_key] = [site]
     # find duplicates, one chromosome at a time
     dups = []
     for chr in by_chr:
@@ -148,9 +149,12 @@ def remove_duplicates(fragile_list, distance):
             # add to positions list if midpoint of j is less than Xbp from i
             # if duplicates are found they will make identical lists for each
             # site in i
-            positions = [j for j in by_chr[chr] if
-                     (int(i[2])+int(i[3]))/2 >= (int(j[2])+int(j[3]))/2 - X and
-                      (int(i[2])+int(i[3]))/2 <= (int(j[2])+int(j[3]))/2 + X]
+            positions = []
+            for j in by_chr[chr]:
+                i_mid = (int(i[2]) + int(i[3])) / 2
+                j_mid = (int(j[2]) + int(j[3])) / 2
+                if i_mid >= j_mid - X and i_mid <= j_mid + X:
+                    positions.append(j)
             # form one entry from each list covering full range of site
             # k = each site in the duplicated positions list.
             # obtain minimum and maximum genomic coordinates across all

notes.md

@@ -0,0 +1,16 @@
+# Good
+- The code might work?
+
+# Bad
+- No packaging integration
+- Can't run tests without 10GB of data?
+- Running tests as described in docs fails with `ImportError`
+- Code doesn't compile `AttributeError: _Environ instance has no __call__ method` cf7140f
+- Code doesn't pass PEP8
+- [Illegible syntax](https://github.com/DeskGen/brkpoints/pull/5#discussion_r24162577)
+- Single character variable names in nested loops aren't readable even if
+  they're not in a convoluted list comp
+- "Predictably" formatted strings used instead of
+  [data](https://docs.python.org/2/library/stdtypes.html#dict)
+  [structures](https://docs.python.org/2/library/stdtypes.html#typesseq)!?
+- Reticent to assign? 438f80a