Reformat contig tables in feature

michaelbarton · Oct 30, 2012 · dc5437b · dc5437b
1 parent 409e1ea
commit dc5437b
Showing 1 changed file with 82 additions and 82 deletions.
diff --git a/features/contigs.feature b/features/contigs.feature
@@ -22,14 +22,14 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          0 |          0 |          0 |     0.00 |   0.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      | All    |          0 |          0 |          0 |     0.00 |   0.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a single contig
@@ -50,15 +50,15 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          4 |          4 |   100.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |          4 |          4 |   100.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |          4 |          4 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a two different contigs
@@ -84,16 +84,16 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          6 |          6 |    50.00 |  66.67 |
-      | contig00002      |          7 |         12 |          6 |    50.00 |  33.33 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |         12 |         12 |   100.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          6 |          6 |    50.00 |  66.67 |
+      |      2 |          7 |         12 |          6 |    50.00 |  33.33 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |         12 |         12 |   100.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a two repeated contigs
@@ -117,16 +117,16 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          6 |          6 |    50.00 |  66.67 |
-      | contig00002      |          7 |         12 |          6 |    50.00 |  66.67 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |         12 |         12 |   100.00 |  66.67 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          6 |          6 |    50.00 |  66.67 |
+      |      2 |          7 |         12 |          6 |    50.00 |  66.67 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |         12 |         12 |   100.00 |  66.67 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a two contigs separated by a gap
@@ -155,16 +155,16 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          6 |          6 |    30.00 |  66.67 |
-      | contig00002      |         15 |         20 |          6 |    30.00 |  33.33 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |         20 |         12 |    60.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          6 |          6 |    30.00 |  66.67 |
+      |      2 |         15 |         20 |          6 |    30.00 |  33.33 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |         20 |         12 |    60.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a two contigs and a gap at the start
@@ -193,16 +193,16 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          9 |         14 |          6 |    30.00 |  66.67 |
-      | contig00002      |         15 |         20 |          6 |    30.00 |  33.33 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          9 |         20 |         12 |    60.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          9 |         14 |          6 |    30.00 |  66.67 |
+      |      2 |         15 |         20 |          6 |    30.00 |  33.33 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          9 |         20 |         12 |    60.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with a two contigs and a gap at the end
@@ -231,16 +231,16 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          6 |          6 |    30.00 |  66.67 |
-      | contig00002      |          7 |         12 |          6 |    30.00 |  33.33 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |         12 |         12 |    60.00 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          6 |          6 |    30.00 |  66.67 |
+      |      2 |          7 |         12 |          6 |    30.00 |  33.33 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |         12 |         12 |    60.00 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: A scaffold with two contigs containing internal gaps separated by a gap
@@ -269,18 +269,18 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      +------------------+------------+------------+------------+----------+--------+
-      |                             Scaffold Contigs                                |
-      +------------------+------------+------------+------------+----------+--------+
-      |     Sequence     | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
-      +------------------+------------+------------+------------+----------+--------+
-      | contig00001      |          1 |          4 |          4 |    13.33 |   0.00 |
-      | contig00002      |          9 |         12 |          4 |    13.33 | 100.00 |
-      | contig00003      |         19 |         22 |          4 |    13.33 |   0.00 |
-      | contig00004      |         27 |         30 |          4 |    13.33 | 100.00 |
-      +------------------+------------+------------+------------+----------+--------+
-      | All              |          1 |         30 |         16 |    53.33 |  50.00 |
-      +------------------+------------+------------+------------+----------+--------+
+      +--------+------------+------------+------------+----------+--------+
+      |                        Scaffold Contigs                           |
+      +--------+------------+------------+------------+----------+--------+
+      | Contig | Start (bp) |  End (bp)  | Size (bp)  | Size (%) | GC (%) |
+      +--------+------------+------------+------------+----------+--------+
+      |      1 |          1 |          4 |          4 |    13.33 |   0.00 |
+      |      2 |          9 |         12 |          4 |    13.33 | 100.00 |
+      |      3 |         19 |         22 |          4 |    13.33 |   0.00 |
+      |      4 |         27 |         30 |          4 |    13.33 | 100.00 |
+      +--------+------------+------------+------------+----------+--------+
+      |    All |          1 |         30 |         16 |    53.33 |  50.00 |
+      +--------+------------+------------+------------+----------+--------+
       """
 
   Scenario: Generating CSV output
@@ -309,8 +309,8 @@ Feature: Producing a summary of the scaffold contigs
      Then the exit status should be 0
       And the output should contain:
       """
-      sequence,start_bp,end_bp,size_bp,size_%,gc_%
-      contig0001,1,6,6,30.00,66.67
-      contig0002,7,12,6,30.00,33.33
+      contig,start_bp,end_bp,size_bp,size_%,gc_%
+      1,1,6,6,30.00,66.67
+      1,7,12,6,30.00,33.33
       all,1,12,12,60.00,50.00
       """