- - - - - - + + + + + + + @@ -126,14 +130,5 @@ 6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832 ]]> - - -@UNPUBLISHED{Seemann2016, - author = {Seemann, Torsten}, - title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, - year = {2016}, - url = {https://github.com/tseemann/abricate}, -} - - + diff -r 6e9aea89e388 -r 78c75f134c16 abricate_list.xml --- a/abricate_list.xml Mon Sep 04 02:47:12 2017 -0400 +++ b/abricate_list.xml Mon Mar 19 10:42:19 2018 -0400 @@ -1,9 +1,12 @@ - - - abricate - - - abricate --version + + + List all of abricate's available databases. + + + macros.xml + + + '$report' @@ -28,14 +31,5 @@ ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder. ]]> - - -@UNPUBLISHED{Seemann2016, - author = {Seemann, Torsten}, - title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, - year = {2016}, - url = {https://github.com/tseemann/abricate}, -} - - + diff -r 6e9aea89e388 -r 78c75f134c16 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 19 10:42:19 2018 -0400 @@ -0,0 +1,27 @@ + + + + abricate + + + + + + + + + 0.8 + + + + + @UNPUBLISHED{Seemann2016, + author = {Seemann, Torsten}, + title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, + year = {2016}, + url = {https://github.com/tseemann/abricate}, + } + + + + diff -r 6e9aea89e388 -r 78c75f134c16 test-data/output_gbk.txt --- a/test-data/output_gbk.txt Mon Sep 04 02:47:12 2017 -0400 +++ b/test-data/output_gbk.txt Mon Mar 19 10:42:19 2018 -0400 @@ -1,2 +1,1 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION -STANORAX 246 1412 norA_1 1-1167/1167 =============== 0/0 100.00 100.00 resfinder M97169 +#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT diff -r 6e9aea89e388 -r 78c75f134c16 test-data/output_list.txt --- a/test-data/output_list.txt Mon Sep 04 02:47:12 2017 -0400 +++ b/test-data/output_list.txt Mon Mar 19 10:42:19 2018 -0400 @@ -1,8 +1,8 @@ DATABASE SEQUENCES DATE -argannot 1749 -card 2153 -ncbi 4124 -ncbibetalactamase 1557 -plasmidfinder 263 -resfinder 2228 -vfdb 2597 +argannot 1749 +card 2220 +ecoh 597 +ncbi 4324 +plasmidfinder 263 +resfinder 2280 +vfdb 2597 diff -r 6e9aea89e388 -r 78c75f134c16 test-data/output_mrsa.txt --- a/test-data/output_mrsa.txt Mon Sep 04 02:47:12 2017 -0400 +++ b/test-data/output_mrsa.txt Mon Mar 19 10:42:19 2018 -0400 @@ -1,9 +1,9 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION -NC_002952.2 40786 41556 aadD_1 1-771/771 =============== 0/0 100.00 99.74 resfinder AF181950 -NC_002952.2 44919 46928 mecA_15 1-2010/2010 =============== 0/0 100.00 100.00 resfinder AB505628 -NC_002952.2 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 -NC_002952.2 56747 57529 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 -NC_002952.2 782414 783580 norA_1 1-1167/1167 =============== 0/0 100.00 91.69 resfinder M97169 -NC_002952.2 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 -NC_002952.2 1797370 1798152 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 -NC_002952.2 1913827 1914672 blaZ_36 1-846/846 =============== 0/0 100.00 100.00 resfinder AJ400722 +#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT + NC_002952.2 40786 41556 aadD_1 1-771/771 =============== 0/0 100.00 99.74 resfinder AF181950 Alternate name; ant(4')-Ia and aadD2 + NC_002952.2 44919 46928 mecA_15 1-2010/2010 =============== 0/0 100.00 100.00 resfinder AB505628 mecA_15 + NC_002952.2 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 + NC_002952.2 56747 57529 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 Alternate name; aad9 ant(9)-Ia + NC_002952.2 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 + NC_002952.2 1797370 1798152 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 Alternate name; aad9 ant(9)-Ia + NC_002952.2 1913827 1914672 blaZ_36 1-846/846 =============== 0/0 100.00 100.00 resfinder AJ400722 blaZ_36 + NC_002952.2 2488459 2488878 fosD_1 1-420/420 =============== 0/0 100.00 79.05 resfinder KC989517 fosD_1 diff -r 6e9aea89e388 -r 78c75f134c16 test-data/output_noheader.txt --- a/test-data/output_noheader.txt Mon Sep 04 02:47:12 2017 -0400 +++ b/test-data/output_noheader.txt Mon Mar 19 10:42:19 2018 -0400 @@ -1,8 +1,8 @@ -NC_002952.2 40786 41556 aadD_1 1-771/771 =============== 0/0 100.00 99.74 resfinder AF181950 -NC_002952.2 44919 46928 mecA_15 1-2010/2010 =============== 0/0 100.00 100.00 resfinder AB505628 -NC_002952.2 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 -NC_002952.2 56747 57529 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 -NC_002952.2 782414 783580 norA_1 1-1167/1167 =============== 0/0 100.00 91.69 resfinder M97169 -NC_002952.2 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 -NC_002952.2 1797370 1798152 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 -NC_002952.2 1913827 1914672 blaZ_36 1-846/846 =============== 0/0 100.00 100.00 resfinder AJ400722 + NC_002952.2 40786 41556 aadD_1 1-771/771 =============== 0/0 100.00 99.74 resfinder AF181950 Alternate name; ant(4')-Ia and aadD2 + NC_002952.2 44919 46928 mecA_15 1-2010/2010 =============== 0/0 100.00 100.00 resfinder AB505628 mecA_15 + NC_002952.2 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 + NC_002952.2 56747 57529 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 Alternate name; aad9 ant(9)-Ia + NC_002952.2 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 + NC_002952.2 1797370 1798152 spc_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 Alternate name; aad9 ant(9)-Ia + NC_002952.2 1913827 1914672 blaZ_36 1-846/846 =============== 0/0 100.00 100.00 resfinder AJ400722 blaZ_36 + NC_002952.2 2488459 2488878 fosD_1 1-420/420 =============== 0/0 100.00 79.05 resfinder KC989517 fosD_1 diff -r 6e9aea89e388 -r 78c75f134c16 test-data/output_noresults.txt --- a/test-data/output_noresults.txt Mon Sep 04 02:47:12 2017 -0400 +++ b/test-data/output_noresults.txt Mon Mar 19 10:42:19 2018 -0400 @@ -1,1 +1,1 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION +#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT