Merge pull request #97 from andrewjpage/nosupport

update no support option in fastml
nickjcroucher · Jan 29, 2014 · c993048 · c993048
2 parents 390a5e0 + 33d98a6
commit c993048
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git a/python/gubbins/common.py b/python/gubbins/common.py
@@ -87,7 +87,7 @@ def parse_and_run(self):
     # Default parameters
     RAXML_EXEC = 'raxmlHPC -f d -p 1 -m GTRGAMMA'
     FASTTREE_EXEC = 'FastTree'
-    FASTTREE_PARAMS = '-gtr -gamma -nt'
+    FASTTREE_PARAMS = '-nosupport -gtr -gamma -nt'
     GUBBINS_EXEC = 'gubbins'
     FASTML_EXEC = 'fastml -mg -qf -b '
 

diff --git a/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.gff b/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.gff
@@ -1,5 +1,5 @@
 ##gff-version 3
 ##sequence-region SEQUENCE 1 242
-SEQUENCE	GUBBINS	CDS	27	107	0.000	.	0	node="N5->N6";neg_log_likelihood="22.985061"taxa=" sequence_5  sequence_3  sequence_2 sequence_4";snp_count="30"
+SEQUENCE	GUBBINS	CDS	51	84	0.000	.	0	node="N5->N6";neg_log_likelihood="8.046578"taxa=" sequence_5  sequence_3  sequence_2 sequence_4";snp_count="30"
 SEQUENCE	GUBBINS	CDS	124	201	0.000	.	0	node="N1->sequence_10";neg_log_likelihood="40.502855"taxa="sequence_10";snp_count="78"
-SEQUENCE	GUBBINS	CDS	0	83	0.000	.	0	node="N1->N2";neg_log_likelihood="20.845063"taxa=" sequence_9  sequence_7 sequence_8";snp_count="22"
+SEQUENCE	GUBBINS	CDS	24	49	0.000	.	0	node="N1->N2";neg_log_likelihood="7.543407"taxa=" sequence_9  sequence_7 sequence_8";snp_count="22"
diff --git a/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.stats b/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.stats
@@ -10,10 +10,10 @@ sequence_8	0	0	0	0	0	0	0.000000	0.000000	242
 sequence_9	0	0	0	0	0	0	0.000000	0.000000	227
 sequence_10	78	102	180	77	154	1	0.764706	0.009804	227
 N3	0	0	0	0	0	0	0.000000	0.000000	242
-N2	22	0	22	83	0	1	0.000000	0.000000	242
+N2	22	0	22	25	0	1	0.000000	0.000000	242
 N8	0	0	0	0	0	0	0.000000	0.000000	242
 N7	0	0	0	0	0	0	0.000000	0.000000	242
-N6	30	0	30	80	0	1	0.000000	0.000000	242
+N6	30	0	30	33	0	1	0.000000	0.000000	242
 N5	0	0	0	0	0	0	0.000000	0.000000	242
 N4	0	0	0	0	0	0	0.000000	0.000000	242
 N1	0	0	0	0	0	0	0.000000	0.000000	242
diff --git a/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.tab b/python/gubbins/tests/data/expected_RAxML_result.multiple_recombinations.iteration_5.tab
@@ -1,6 +1,6 @@
-FT   misc_feature    27..107
+FT   misc_feature    51..84
 FT                   /node="N5->N6"
-FT                   /neg_log_likelihood=22.985061
+FT                   /neg_log_likelihood=8.046578
 FT                   /colour=2
 FT                   /taxa=" sequence_5  sequence_3  sequence_2 sequence_4"
 FT                   /SNP_count=30
@@ -10,9 +10,9 @@ FT                   /neg_log_likelihood=40.502855
 FT                   /colour=4
 FT                   /taxa="sequence_10"
 FT                   /SNP_count=78
-FT   misc_feature    0..83
+FT   misc_feature    24..49
 FT                   /node="N1->N2"
-FT                   /neg_log_likelihood=20.845063
+FT                   /neg_log_likelihood=7.543407
 FT                   /colour=2
 FT                   /taxa=" sequence_9  sequence_7 sequence_8"
 FT                   /SNP_count=22