EI-CoreBioinformatics#136: fixed the tests

lucventurini · Nov 27, 2019 · f871716 · f871716
1 parent 8d5cb1c
commit f871716
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/Mikado/configuration/daijin_configurator.py b/Mikado/configuration/daijin_configurator.py
@@ -176,7 +176,7 @@ def create_daijin_config(args, level="ERROR", piped=False):
     logger = create_default_logger("daijin_config", level=level)
 
     config = create_daijin_base_config(simple=(not args.full))
-    if args.seed is not None:
+    if args.seed is not None and isinstance(args.seed, int) and args.seed not in (True, False):
         config["seed"] = args.seed
     assert "reference" in config, config.keys()
     config["reference"]["genome"] = args.genome

diff --git a/Mikado/tests/check_seed.yaml b/Mikado/tests/check_seed.yaml
@@ -187,6 +187,7 @@ serialise:
     output_dir: .
     transcripts: mikado_prepared.fasta
     xml: []
+  codon_table: 0
   max_regression: 0.1
   procs: 1
 short_reads:

diff --git a/Mikado/tests/test_external/mikado.configuration.testds.yaml b/Mikado/tests/test_external/mikado.configuration.testds.yaml
@@ -243,6 +243,8 @@ prepare:
     - Rmai_coding.gff
     - Rpad_coding.gff
     - Sfuc_coding.gff
+  minimum_cdna_length: 200
+  max_intron_length: 1000000
   lenient: false
   procs: 1
   strand_specific: false
@@ -269,6 +271,6 @@ serialise:
     output_dir: Testds
     transcripts: mikado_prepared.testds.fasta
     xml: []
+  codon_table: 0
   max_regression: 0.1
   procs: 1
-