Output ctg_cov column

sanger-pathogens · Mar 31, 2017 · 9e490ce · 9e490ce
1 parent 15a88c8
commit 9e490ce
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Showing 4 changed files with 24 additions and 23 deletions.
diff --git a/ariba/summary.py b/ariba/summary.py
@@ -122,6 +122,7 @@ def _gather_unfiltered_output_data(self):
                             'match': 'no',
                             'novel_var': 'NA',
                             'pct_id': 'NA',
+                            'ctg_cov': 'NA',
                             'ref_seq': 'NA'
                     }
                 else:
@@ -164,11 +165,11 @@ def _to_matrix(cls, filenames, all_data, all_potential_columns, cluster_cols):
         matrix = []
         making_header_lines = True
         phandango_header = ['name']
-        phandango_suffixes = {'assembled': ':o1', 'match': ':o1', 'ref_seq': ':o2', 'pct_id': ':c1', 'known_var': ':o1', 'novel_var': ':o1'}
+        phandango_suffixes = {'assembled': ':o1', 'match': ':o1', 'ref_seq': ':o2', 'pct_id': ':c1', 'ctg_cov': ':c3', 'known_var': ':o1', 'novel_var': ':o1'}
         ref_seq_counter = 2
         csv_header = ['name']
-        summary_cols_in_order = ['assembled', 'match', 'ref_seq', 'pct_id', 'known_var', 'novel_var']
-        summary_cols_set = set(['assembled', 'match', 'ref_seq', 'pct_id', 'known_var', 'novel_var'])
+        summary_cols_in_order = ['assembled', 'match', 'ref_seq', 'pct_id', 'ctg_cov', 'known_var', 'novel_var']
+        summary_cols_set = set(['assembled', 'match', 'ref_seq', 'pct_id', 'ctg_cov', 'known_var', 'novel_var'])
         summary_cols_in_order = [x for x in summary_cols_in_order if cluster_cols[x]]
 
         for filename in sorted(filenames):

diff --git a/ariba/tests/data/summary_test_whole_run.out.csv b/ariba/tests/data/summary_test_whole_run.out.csv
@@ -1,3 +1,3 @@
-name,23S.assembled,23S.match,23S.ref_seq,23S.pct_id,23S.known_var,23S.2597CT,23S.2597CT.%,23S.2597TC,23S.2597TC.%,coding1.assembled,coding1.match,coding1.ref_seq,coding1.pct_id,coding2.assembled,coding2.match,coding2.ref_seq,coding2.pct_id,coding3.assembled,coding3.match,coding3.ref_seq,coding3.pct_id,coding5.assembled,coding5.match,coding5.ref_seq,coding5.pct_id,coding5.known_var,coding5.A42S,coding6.assembled,coding6.match,coding6.ref_seq,coding6.pct_id,coding6.known_var,coding6.A52S,coding7.assembled,coding7.ref_seq,coding7.pct_id,coding8.assembled,coding8.match,coding8.ref_seq,coding8.pct_id,coding8.novel_var,coding8.A53S,mdfA.assembled,mdfA.ref_seq,mdfA.pct_id,mdfA.novel_var,noncoding1.assembled,noncoding1.match,noncoding1.ref_seq,noncoding1.pct_id,noncoding10.assembled,noncoding10.match,noncoding10.ref_seq,noncoding10.pct_id,noncoding10.novel_var,noncoding10.100T,noncoding10.100T.%,noncoding11.assembled,noncoding11.match,noncoding11.ref_seq,noncoding11.pct_id,noncoding11.novel_var,noncoding11.101AG,noncoding11.101AG.%,noncoding2.assembled,noncoding2.match,noncoding2.ref_seq,noncoding2.pct_id,noncoding3.assembled,noncoding3.match,noncoding3.ref_seq,noncoding3.pct_id,noncoding5.assembled,noncoding5.match,noncoding5.ref_seq,noncoding5.pct_id,noncoding5.known_var,noncoding5.42T,noncoding5.42T.%,noncoding6.assembled,noncoding6.match,noncoding6.ref_seq,noncoding6.pct_id,noncoding6.known_var,noncoding6.52CT,noncoding6.52CT.%,noncoding7.assembled,noncoding7.match,noncoding7.ref_seq,noncoding7.pct_id,noncoding7.known_var,noncoding7.53T,noncoding7.53T.%,noncoding8.assembled,noncoding8.match,noncoding8.ref_seq,noncoding8.pct_id,noncoding9.assembled,noncoding9.ref_seq,noncoding9.pct_id
-summary_test_whole_run.in.1.tsv,yes,yes,23S.rDNA_WHO_F_01358c,99.86,yes,no,NA,yes,100.0,interrupted,no,coding1_ref1,99.1,yes,yes,coding2_ref1,98.2,no,no,NA,NA,yes,no,coding5_ref1,97.4,no,no,yes,yes,coding6_ref1,95.5,yes,yes,yes,coding7_ref1,95.4,yes,yes,coding8_ref1,95.3,yes,yes,interrupted,mdfA.3001328.JQ394987.0_1233.561,97.0,yes,yes,yes,noncoding1_ref1,99.1,yes,yes,noncoding10_ref1,95.1,yes,yes,99.0,yes,yes,noncoding11_ref1,95.05,het,het,30.0,yes,yes,noncoding2_ref1,98.2,no,no,NA,NA,yes,yes,noncoding5_ref1,97.4,yes,yes,100.0,yes,yes,noncoding6_ref1,95.5,yes,het,70.0,yes,yes,noncoding7_ref1,95.4,yes,yes,98.6,yes,yes,noncoding8_ref1,95.3,yes,noncoding9_ref1,95.2
-summary_test_whole_run.in.2.tsv,yes_nonunique,no,23S.rDNA_WHO_F_01358c,99.84,het,het,12.8,no,NA,yes,yes,coding1_ref2,99.2,no,no,NA,NA,yes,yes,coding3_ref1,97.6,yes,yes,coding5_ref1,97.4,yes,yes,no,no,NA,NA,NA,NA,no,NA,NA,no,no,NA,NA,NA,NA,no,NA,NA,NA,yes,yes,noncoding1_ref2,99.2,no,no,NA,NA,NA,NA,NA,no,no,NA,NA,NA,NA,NA,no,no,NA,NA,yes,yes,noncoding3_ref1,97.6,yes,no,noncoding5_ref1,99.42,no,no,NA,no,no,NA,NA,NA,NA,NA,no,no,NA,NA,NA,NA,NA,no,no,NA,NA,no,NA,NA
+name,23S.assembled,23S.match,23S.ref_seq,23S.pct_id,23S.ctg_cov,23S.known_var,23S.2597CT,23S.2597CT.%,23S.2597TC,23S.2597TC.%,coding1.assembled,coding1.match,coding1.ref_seq,coding1.pct_id,coding1.ctg_cov,coding2.assembled,coding2.match,coding2.ref_seq,coding2.pct_id,coding2.ctg_cov,coding3.assembled,coding3.match,coding3.ref_seq,coding3.pct_id,coding3.ctg_cov,coding5.assembled,coding5.match,coding5.ref_seq,coding5.pct_id,coding5.ctg_cov,coding5.known_var,coding5.A42S,coding6.assembled,coding6.match,coding6.ref_seq,coding6.pct_id,coding6.ctg_cov,coding6.known_var,coding6.A52S,coding7.assembled,coding7.ref_seq,coding7.pct_id,coding7.ctg_cov,coding8.assembled,coding8.match,coding8.ref_seq,coding8.pct_id,coding8.ctg_cov,coding8.novel_var,coding8.A53S,mdfA.assembled,mdfA.ref_seq,mdfA.pct_id,mdfA.ctg_cov,mdfA.novel_var,noncoding1.assembled,noncoding1.match,noncoding1.ref_seq,noncoding1.pct_id,noncoding1.ctg_cov,noncoding10.assembled,noncoding10.match,noncoding10.ref_seq,noncoding10.pct_id,noncoding10.ctg_cov,noncoding10.novel_var,noncoding10.100T,noncoding10.100T.%,noncoding11.assembled,noncoding11.match,noncoding11.ref_seq,noncoding11.pct_id,noncoding11.ctg_cov,noncoding11.novel_var,noncoding11.101AG,noncoding11.101AG.%,noncoding2.assembled,noncoding2.match,noncoding2.ref_seq,noncoding2.pct_id,noncoding2.ctg_cov,noncoding3.assembled,noncoding3.match,noncoding3.ref_seq,noncoding3.pct_id,noncoding3.ctg_cov,noncoding5.assembled,noncoding5.match,noncoding5.ref_seq,noncoding5.pct_id,noncoding5.ctg_cov,noncoding5.known_var,noncoding5.42T,noncoding5.42T.%,noncoding6.assembled,noncoding6.match,noncoding6.ref_seq,noncoding6.pct_id,noncoding6.ctg_cov,noncoding6.known_var,noncoding6.52CT,noncoding6.52CT.%,noncoding7.assembled,noncoding7.match,noncoding7.ref_seq,noncoding7.pct_id,noncoding7.ctg_cov,noncoding7.known_var,noncoding7.53T,noncoding7.53T.%,noncoding8.assembled,noncoding8.match,noncoding8.ref_seq,noncoding8.pct_id,noncoding8.ctg_cov,noncoding9.assembled,noncoding9.ref_seq,noncoding9.pct_id,noncoding9.ctg_cov
+summary_test_whole_run.in.1.tsv,yes,yes,23S.rDNA_WHO_F_01358c,99.86,744.8,yes,no,NA,yes,100.0,interrupted,no,coding1_ref1,99.1,10.1,yes,yes,coding2_ref1,98.2,42.42,no,no,NA,NA,NA,yes,no,coding5_ref1,97.4,14.1,no,no,yes,yes,coding6_ref1,95.5,24.32,yes,yes,yes,coding7_ref1,95.4,24.32,yes,yes,coding8_ref1,95.3,24.31,yes,yes,interrupted,mdfA.3001328.JQ394987.0_1233.561,97.0,16.2,yes,yes,yes,noncoding1_ref1,99.1,10.1,yes,yes,noncoding10_ref1,95.1,24.27,yes,yes,99.0,yes,yes,noncoding11_ref1,95.05,24.26,het,het,30.0,yes,yes,noncoding2_ref1,98.2,42.42,no,no,NA,NA,NA,yes,yes,noncoding5_ref1,97.4,14.1,yes,yes,100.0,yes,yes,noncoding6_ref1,95.5,24.32,yes,het,70.0,yes,yes,noncoding7_ref1,95.4,24.31,yes,yes,98.6,yes,yes,noncoding8_ref1,95.3,24.29,yes,noncoding9_ref1,95.2,24.28
+summary_test_whole_run.in.2.tsv,yes_nonunique,no,23S.rDNA_WHO_F_01358c,99.84,344.0,het,het,12.8,no,NA,yes,yes,coding1_ref2,99.2,10.1,no,no,NA,NA,NA,yes,yes,coding3_ref1,97.6,37.6,yes,yes,coding5_ref1,97.4,14.1,yes,yes,no,no,NA,NA,NA,NA,NA,no,NA,NA,NA,no,no,NA,NA,NA,NA,NA,no,NA,NA,NA,NA,yes,yes,noncoding1_ref2,99.2,10.1,no,no,NA,NA,NA,NA,NA,NA,no,no,NA,NA,NA,NA,NA,NA,no,no,NA,NA,NA,yes,yes,noncoding3_ref1,97.6,37.6,yes,no,noncoding5_ref1,99.42,14.1,no,no,NA,no,no,NA,NA,NA,NA,NA,NA,no,no,NA,NA,NA,NA,NA,NA,no,no,NA,NA,NA,no,NA,NA,NA