extended README

CHANGELOG

@@ -1,3 +1,3 @@
 Version 0.0.1 of SeroBA
-Version 0.1.3 of SeroBA: commandline parameter parser for k-mer coverage, adding updated database to SeroBA including serotypes 6E, 6F, 11E, 10X, 39X and two NT references
+Version 0.1.3 of SeroBA: commandline parameter parser for k-mer coverage, adding updated database to SeroBA including serotypes 6E, 6F, 11E, 10X, 39X, 35D and two NT references
 Version 0.1.4 bug fix with serogroup 6 and 11, bug fix unittest in for createDBs

README.md

@@ -3,12 +3,12 @@ SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS read
 ## Usage
 Since SeroBA v0.1.3 an updated variant of the CTV from PneumoCat is provided in the SeroBA package. This includes the serotypes 6E, 6F, 11E, 10X, 39X and two NT references. It is not necessary to use SeroBA getPneumocat. You can directly start with seroba createDBs with the database folder from this repository. It is recommended to make a working copy of it.
 ```
-usage: seroba  getPneumocat out_dir
+usage: seroba  getPneumocat <database dir>
 
 Downloads PneumoCat and build an tsv formatted meta data file out of it
 
 positional arguments:
-  out_dir      directory to store the PneumoCats capsular type variant (CTV) database
+  database dir      directory to store the PneumoCats capsular type variant (CTV) database
 
 
 usage: seroba createDBs  <database dir> <kmer size>
@@ -21,12 +21,14 @@ positional arguments:
 
     usage: seroba runSerotyping [options]  <databases directory> <read1> <read2> <prefix>
 
-    identify serotype of your input data
+    Example : seroba createDBs my_database/ 71
+
+Identify serotype of your input data
 
     positional arguments:
-      databases          path to database directory
+      database dir         path to database directory
       read1              forward read file
-      read2              backward read file
+      read2              reverse read file
       prefix             unique prefix
 
     optional arguments:
@@ -39,6 +41,7 @@ positional arguments:
 
 
 
+
 Summaries the output in one tsv file
 
 usage: seroba summary  <output folder>
@@ -54,7 +57,8 @@ In the folder 'prefix' you will find a pred.tsv including your predicted serotyp
 as well as en file called detailed_serogroup_info.txt including information about
 snps, genes, and alleles that are found in your reads.
 After the use of "seroba summary" a tsv file called summary.tsv is created that
-consists of two columns (sample Id , serotype).
+consists of three columns (sample Id , serotype, comments).
+Serotypes that do not match any reference are marked as "untypable"(v0.1.3).
 
 ## Database
 You can use the CTV von PneumoCat by using seroba  getPneumocat. It is also

pneumocat_db_test.tsv

@@ -0,0 +1,49 @@
+01	01	01	1	ref
+06A	06A	06A	1	ref
+06B	06A	06B	1	ref
+06C	06A	06C	1	ref
+06D	06A	06D	1	ref
+06E	06A	06E	1	ref
+07A	07A	07A	1	ref
+07B	07B	07B	1	ref
+07C	07B	07C	1	ref
+07F	07A	07F	1	ref
+40	07B	40	1	ref
+wciN-1	06A	06A	0	allele
+wciN-1	06A	06B	0	allele
+wciN-2	06A	06C	0	allele
+wciN-2	06A	06D	0	allele
+wciN-3	06A	06E	0	allele
+wciP_06A	06A	06A	0	snps	583	AGT
+wciP_06B	06A	06B	0	snps	583	AAT
+wciP_06C	06A	06C	0	snps	583	AGT
+wciP_06D	06A	06D	0	snps	583	AAT
+wcwD	07A	07A	1	pseudo	1
+wcwD	07A	07F	1	pseudo	0
+wcwK_07B	07B	07B	0	snps	145	CTT
+wcwK_07B	07B	07B	0	snps	385	TTT
+wcwK_07B	07B	07B	0	snps	46	GAT
+wcwK_07B	07B	07B	0	snps	487	ACT
+wcwK_07B	07B	07B	0	snps	706	CAT
+wcwK_07B	07B	07B	0	snps	880	CTT
+wcwK_07B	07B	07B	0	snps	928	AAT
+wcwK_07B	07B	07B	0	snps	937	GCA
+wcwK_07B	07B	07B	0	snps	946	GGT
+wcwK_07C	07B	07C	0	snps	145	CTT
+wcwK_07C	07B	07C	0	snps	385	TGT
+wcwK_07C	07B	07C	0	snps	46	GGT
+wcwK_07C	07B	07C	0	snps	487	GCT
+wcwK_07C	07B	07C	0	snps	706	CAT
+wcwK_07C	07B	07C	0	snps	880	CTT
+wcwK_07C	07B	07C	0	snps	928	AAT
+wcwK_07C	07B	07C	0	snps	937	GAA
+wcwK_07C	07B	07C	0	snps	946	GGT
+wcwK_40	07B	40	0	snps	145	TTT
+wcwK_40	07B	40	0	snps	385	ACT
+wcwK_40	07B	40	0	snps	46	AAT
+wcwK_40	07B	40	0	snps	487	ACT
+wcwK_40	07B	40	0	snps	706	TAT
+wcwK_40	07B	40	0	snps	880	TTT
+wcwK_40	07B	40	0	snps	928	AGT
+wcwK_40	07B	40	0	snps	937	GAA
+wcwK_40	07B	40	0	snps	946	GAT

scripts/seroba

@@ -15,7 +15,7 @@ subparsers = parser.add_subparsers(title='Available commands', help='', metavar=
 subparser_getPneumocat = subparsers.add_parser(
     'getPneumocat',
     help='downloads genetic information from PneumoCat',
-    usage='seroba getPneumocat  <out_dir>',
+    usage='seroba getPneumocat  <database dir>',
     description='Downlaods PneumoCat and build an tsv formated meta data file out of it',
 )
 subparser_getPneumocat.add_argument('out_dir', type=str, \

seroba/tasks/getPneumocat.py

@@ -3,5 +3,5 @@
 
 
 def run(options):
-    pneumo = get_pneumocat_data.GetPneumocatData(options.out_dir)
+    pneumo = get_pneumocat_data.GetPneumocatData(options.database_dir)
     pneumo.run()

seroba/tests/data/09V/detailed_serogroup_info.txt

@@ -2,14 +2,14 @@ Predicted Serotype:	09V
 Serotype predicted by ariba	:09A
 assembly from ariba as an identiy of: 	99.99	 with this serotype
 Serotype 	 Genetic Variant
-09L	snps	['wcjA', '852', 'GCA']
-09L	snps	['wcjA', '429', 'GGT']
-09L	snps	['wcjA', '528', 'GAT']
-09L	snps	['wcjA', '636', 'GAT']
-09L	genes	wcjD
-09N	snps	['wcjA', '957', 'ACT']
-09N	snps	['wcjA', '414', 'TAT']
-09N	genes	wcjD
-09V	pseudo	wcjE
 09V	genes	wcjD
+09V	pseudo	wcjE
+09N	genes	wcjD
+09N	snps	['wcjA', '414', 'TAT']
+09N	snps	['wcjA', '957', 'ACT']
 09A	genes	wcjD
+09L	genes	wcjD
+09L	snps	['wcjA', '852', 'GCA']
+09L	snps	['wcjA', '636', 'GAT']
+09L	snps	['wcjA', '528', 'GAT']
+09L	snps	['wcjA', '429', 'GGT']

seroba/tests/data/15B_C/detailed_serogroup_info.txt

@@ -3,5 +3,5 @@ Serotype predicted by ariba	:15C
 assembly from ariba as an identiy of: 	99.38	 with this serotype
 Serotype 	 Genetic Variant
 15B	pseudo	wciZ
-15C	allele	wzd
-15C	allele	wchL
+15B	allele	wzd
+15B	allele	wchL

seroba/tests/data/ERR1438851/detailed_serogroup_info.txt

@@ -2,14 +2,14 @@ Predicted Serotype:	09N
 Serotype predicted by ariba	:09L
 assembly from ariba as an identiy of: 	99.53	 with this serotype
 Serotype 	 Genetic Variant
-09N	snps	['wcjB', '789', 'ACC']
+09V	pseudo	wcjE
 09N	snps	['wzy', '846', 'AAC']
-09N	snps	['wchA', '504', 'TCT']
-09N	snps	['wchA', '879', 'TCA']
-09N	snps	['wcjA', '957', 'ACT']
 09N	snps	['wcjA', '852', 'TCA']
-09N	snps	['wcjA', '429', 'AGT']
 09N	snps	['wcjA', '414', 'TAT']
-09N	snps	['wcjA', '528', 'GGT']
 09N	snps	['wcjA', '636', 'AAT']
-09V	pseudo	wcjE
+09N	snps	['wcjA', '528', 'GGT']
+09N	snps	['wcjA', '429', 'AGT']
+09N	snps	['wcjA', '957', 'ACT']
+09N	snps	['wchA', '879', 'TCA']
+09N	snps	['wchA', '504', 'TCT']
+09N	snps	['wcjB', '789', 'ACC']

seroba/tests/data/ERR1439287/detailed_serogroup_info.txt

@@ -2,18 +2,18 @@ Predicted Serotype:	07C
 Serotype predicted by ariba	:07C
 assembly from ariba as an identiy of: 	99.86	 with this serotype
 Serotype 	 Genetic Variant
-07B	snps	['wcwK', '928', 'AAT']
-07B	snps	['wcwK', '946', 'GGT']
-07B	snps	['wcwK', '880', 'CTT']
-07B	snps	['wcwK', '706', 'CAT']
-07B	snps	['wcwK', '145', 'CTT']
-40	snps	['wcwK', '937', 'GAA']
-07C	snps	['wcwK', '928', 'AAT']
+07C	snps	['wcwK', '385', 'TGT']
 07C	snps	['wcwK', '937', 'GAA']
+07C	snps	['wcwK', '46', 'GGT']
 07C	snps	['wcwK', '946', 'GGT']
 07C	snps	['wcwK', '880', 'CTT']
-07C	snps	['wcwK', '706', 'CAT']
-07C	snps	['wcwK', '46', 'GGT']
+07C	snps	['wcwK', '928', 'AAT']
 07C	snps	['wcwK', '487', 'GCT']
 07C	snps	['wcwK', '145', 'CTT']
-07C	snps	['wcwK', '385', 'TGT']
+07C	snps	['wcwK', '706', 'CAT']
+40	snps	['wcwK', '937', 'GAA']
+07B	snps	['wcwK', '946', 'GGT']
+07B	snps	['wcwK', '880', 'CTT']
+07B	snps	['wcwK', '928', 'AAT']
+07B	snps	['wcwK', '145', 'CTT']
+07B	snps	['wcwK', '706', 'CAT']

seroba/tests/data/ERR1439321/detailed_serogroup_info.txt

@@ -2,11 +2,11 @@ Predicted Serotype:	11A
 Serotype predicted by ariba	:11A
 assembly from ariba as an identiy of: 	99.17	 with this serotype
 Serotype 	 Genetic Variant
-11C	pseudo	gct
 11C	genes	wcwC_11A
-11A	snps	['wcrL', '334', 'AAT']
-11A	pseudo	gct
+11C	pseudo	gct
+11D	genes	wcwC_11A
+11D	pseudo	gct
 11A	genes	wcwC_11A
+11A	pseudo	gct
+11A	snps	['wcrL', '334', 'AAT']
 11B	genes	wcwC_11A
-11D	pseudo	gct
-11D	genes	wcwC_11A

seroba/tests/data/ERR1440275/detailed_serogroup_info.txt

@@ -2,15 +2,15 @@ Predicted Serotype:	09L
 Serotype predicted by ariba	:09L
 assembly from ariba as an identiy of: 	99.98	 with this serotype
 Serotype 	 Genetic Variant
-09L	snps	['wcjB', '789', 'GCC']
+09V	pseudo	wcjE
+09A	pseudo	wcjE
 09L	snps	['wzy', '846', 'GAC']
-09L	snps	['wchA', '504', 'TAT']
-09L	snps	['wchA', '879', 'CCA']
-09L	snps	['wcjA', '957', 'ATT']
 09L	snps	['wcjA', '852', 'GCA']
-09L	snps	['wcjA', '429', 'GGT']
 09L	snps	['wcjA', '414', 'CAT']
-09L	snps	['wcjA', '528', 'GAT']
 09L	snps	['wcjA', '636', 'GAT']
-09V	pseudo	wcjE
-09A	pseudo	wcjE
+09L	snps	['wcjA', '528', 'GAT']
+09L	snps	['wcjA', '429', 'GGT']
+09L	snps	['wcjA', '957', 'ATT']
+09L	snps	['wchA', '879', 'CCA']
+09L	snps	['wchA', '504', 'TAT']
+09L	snps	['wcjB', '789', 'GCC']