Mercurial > repos > iuc > abricate
changeset 7:4efdca267d51 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 6535538b7767c3bbe20ac7e89b682154b595c932"
| author | iuc |
|---|---|
| date | Tue, 29 Oct 2019 19:24:59 -0400 |
| parents | 1bb2ba6d3d96 |
| children | b734db305578 |
| files | macros.xml test-data/output_db-card.txt test-data/output_gbk.txt test-data/output_list.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_noheader.txt test-data/output_noresults.txt |
| diffstat | 8 files changed, 43 insertions(+), 52 deletions(-) [+] |
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--- a/macros.xml Mon Oct 07 14:57:31 2019 -0400 +++ b/macros.xml Tue Oct 29 19:24:59 2019 -0400 @@ -10,7 +10,7 @@ <version_command><![CDATA[abricate --version]]></version_command> </xml> - <token name="@VERSION@">0.9.7</token> + <token name="@VERSION@">0.9.8</token> <xml name="citations"> <citations>
--- a/test-data/output_db-card.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_db-card.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,18 +1,18 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT -MRSA0252.fna gi|49482253|ref|NC_002952.2| 40786 41547 ANT(4')-Ib 1-762/762 =============== 0/0 100.00 100.00 card GQ900432.1:26738-27500 Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides -MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 mecA 1-2007/2007 =============== 0/0 100.00 99.90 card KC243783:1-2008 A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 47025 48782 mecR1 1-1758/1758 =============== 0/0 100.00 99.94 card CP000703.1:40849-42607 mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA/mecR1/mecI operon. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 48782 49153 mecI 1-372/372 =============== 0/0 100.00 99.73 card BA000018.3:48894-49266 mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 ErmA 1-732/732 =============== 0/0 100.00 100.00 card X03216.1:4551-5283 ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 152865 154217 tet(38) 1-1353/1353 =============== 0/0 100.00 98.52 card AY825285:1-1354 Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 376045 376464 mepR 1-420/420 =============== 0/0 100.00 99.05 card BA000017.4:379932-380352 MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 376571 377926 mepA 1-1356/1356 =============== 0/0 100.00 98.53 card AY661734.1:840-2196 MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance while it has also been shown to decrease tigecycline susceptibility. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 774312 774755 mgrA 1-444/444 =============== 0/0 100.00 99.78 card BA000018.3:735417-735861 MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 782414 783579 Staphylococcus_aureus_norA 1-1166/1167 =============== 0/0 99.91 91.51 card D90119.1:478-1645 NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1486310 1487665 arlS 1-1356/1356 =============== 0/0 100.00 98.38 card CP000253.1:1360281-1361637 ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1487662 1488321 arlR 1-660/660 =============== 0/0 100.00 99.09 card NC_009641.1:1461589-1462249 ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 ErmA 1-732/732 =============== 0/0 100.00 100.00 card X03216.1:4551-5283 ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1913827 1914672 PC1_beta-lactamase_(blaZ) 1-846/846 =============== 0/0 100.00 97.16 card CP000732.1:9683-10529 The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus. -MRSA0252.fna gi|49482253|ref|NC_002952.2| 2338959 2340402 Staphylococcys_aureus_LmrS 1-1443/1443 ========/====== 1/1 100.00 91.41 card CP000046.1:2235375-2236818 MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid -MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 Staphylococcus_aureus_FosB 1-420/420 =============== 0/0 100.00 98.81 card AHLO01000073.1:63139-63559 The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein -MRSA0252.fna gi|49482253|ref|NC_002952.2| 2622988 2624175 DHA-1 1-1188/1188 =============== 0/0 100.00 99.16 card BA000018.3:2517801-2518989 DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +MRSA0252.fna gi|49482253|ref|NC_002952.2| 40786 41547 - ANT(4')-Ib 1-762/762 =============== 0/0 100.00 100.00 card GQ900432.1:26738-27500 Kanamycin nucleotidyltransferase sequence from Staphylococcus aureus plasmid. Confers resistance to kanamycin neomycin and other aminoglycosides aminoglycoside +MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 - mecA 1-2007/2007 =============== 0/0 100.00 99.90 card KC243783:1-2008 A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams. penam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 47025 48782 + mecR1 1-1758/1758 =============== 0/0 100.00 99.94 card CP000703.1:40849-42607 mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA/mecR1/mecI operon. penam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 48782 49153 + mecI 1-372/372 =============== 0/0 100.00 99.73 card BA000018.3:48894-49266 mecI acts as a repressor of transcription of the mecA/mecR1/mecI operon. penam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 + ErmA 1-732/732 =============== 0/0 100.00 100.00 card X03216.1:4551-5283 ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA. streptogramin/macrolide/lincosamide +MRSA0252.fna gi|49482253|ref|NC_002952.2| 152865 154217 + tet(38) 1-1353/1353 =============== 0/0 100.00 98.52 card AY825285:1-1354 Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB. benzalkonium_chloride/isoniazid/lincosamide/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/penam/macrolide/nucleoside/nitroimidazole/rifamycin/peptide/rhodamine/tetracycline/oxazolidinone/acridine_dye/fluoroquinolone/cephalosporin/phenicol/glycylcycline/fosfomycin +MRSA0252.fna gi|49482253|ref|NC_002952.2| 376045 376464 + mepR 1-420/420 =============== 0/0 100.00 99.05 card BA000017.4:379932-380352 MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon. glycylcycline/acridine_dye/tetracycline/fluoroquinolone +MRSA0252.fna gi|49482253|ref|NC_002952.2| 376571 377926 + mepA 1-1356/1356 =============== 0/0 100.00 98.53 card AY661734.1:840-2196 MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance while it has also been shown to decrease tigecycline susceptibility. glycylcycline/acridine_dye/tetracycline/fluoroquinolone +MRSA0252.fna gi|49482253|ref|NC_002952.2| 774312 774755 - mgrA 1-444/444 =============== 0/0 100.00 99.78 card BA000018.3:735417-735861 MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38. antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/isoniazid/lincosamide/benzalkonium_chloride/rifamycin/pleuromutilin/nitroimidazole/nucleoside/macrolide/penam/rhodamine/peptide/fosfomycin/glycylcycline/phenicol/cephalosporin/fluoroquinolone/tetracycline/acridine_dye/oxazolidinone +MRSA0252.fna gi|49482253|ref|NC_002952.2| 782414 783579 + Staphylococcus_aureus_norA 1-1166/1167 =============== 0/0 99.91 91.51 card D90119.1:478-1645 NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli. macrolide/penam/nucleoside/rifamycin/nitroimidazole/isoniazid/lincosamide/benzalkonium_chloride/diaminopyrimidine/antibacterial_free_fatty_acids/bicyclomycin/tetracycline/oxazolidinone/acridine_dye/cephalosporin/fluoroquinolone/glycylcycline/phenicol/fosfomycin/peptide/rhodamine +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1486310 1487665 - arlS 1-1356/1356 =============== 0/0 100.00 98.38 card CP000253.1:1360281-1361637 ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression. antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/isoniazid/lincosamide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/rhodamine/peptide/fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/oxazolidinone/acridine_dye +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1487662 1488321 - arlR 1-660/660 =============== 0/0 100.00 99.09 card NC_009641.1:1461589-1462249 ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS. fosfomycin/phenicol/glycylcycline/fluoroquinolone/cephalosporin/tetracycline/acridine_dye/oxazolidinone/rhodamine/peptide/nitroimidazole/rifamycin/nucleoside/penam/macrolide/antibacterial_free_fatty_acids/bicyclomycin/diaminopyrimidine/benzalkonium_chloride/lincosamide/isoniazid +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 + ErmA 1-732/732 =============== 0/0 100.00 100.00 card X03216.1:4551-5283 ErmA confers the MLSb phenotype. Similar to ErmC Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present it binds the leader peptide causing a change in conformation allowing for the expression of ErmA. streptogramin/macrolide/lincosamide +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1913827 1914672 + PC1_beta-lactamase_(blaZ) 1-846/846 =============== 0/0 100.00 97.16 card CP000732.1:9683-10529 The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus. penam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 2338959 2340402 - Staphylococcys_aureus_LmrS 1-1443/1443 ========/====== 1/1 100.00 91.41 card CP000046.1:2235375-2236818 MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid nucleoside/rifamycin/nitroimidazole/macrolide/penam/diaminopyrimidine/bicyclomycin/antibacterial_free_fatty_acids/isoniazid/lincosamide/benzalkonium_chloride/glycylcycline/phenicol/fosfomycin/acridine_dye/oxazolidinone/tetracycline/cephalosporin/fluoroquinolone/aminoglycoside/peptide/rhodamine +MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 + Staphylococcus_aureus_FosB 1-420/420 =============== 0/0 100.00 98.81 card AHLO01000073.1:63139-63559 The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein fosfomycin +MRSA0252.fna gi|49482253|ref|NC_002952.2| 2622988 2624175 - DHA-1 1-1188/1188 =============== 0/0 100.00 99.16 card BA000018.3:2517801-2518989 DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica cephamycin/cephalosporin
--- a/test-data/output_gbk.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_gbk.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,1 +1,1 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE
--- a/test-data/output_list.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_list.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,9 +1,9 @@ DATABASE SEQUENCES DBTYPE DATE -ncbi 5029 nucl 2019-Sep-7 -resfinder 3077 nucl 2019-Sep-7 -card 2594 nucl 2019-Sep-7 -vfdb 2597 nucl 2019-Sep-7 -argannot 2223 nucl 2019-Sep-7 -plasmidfinder 263 nucl 2019-Sep-7 -ecoli_vf 2701 nucl 2019-Sep-7 -ecoh 597 nucl 2019-Sep-7 +ncbi 5029 nucl 2019-Sep-10 +resfinder 3077 nucl 2019-Sep-10 +card 2594 nucl 2019-Sep-10 +vfdb 2597 nucl 2019-Sep-10 +argannot 2223 nucl 2019-Sep-10 +plasmidfinder 460 nucl 2019-Sep-10 +ecoli_vf 2701 nucl 2019-Sep-10 +ecoh 597 nucl 2019-Sep-10
--- a/test-data/output_minid100.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_minid100.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,6 +1,6 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT -MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 mecA_6 1-2007/2007 =============== 0/0 100.00 100.00 resfinder BX571856 mecA_6 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 56747 57529 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1797370 1798152 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE +MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 - mecA_6 1-2007/2007 =============== 0/0 100.00 100.00 resfinder BX571856 mecA Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 + erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A) Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S +MRSA0252.fna gi|49482253|ref|NC_002952.2| 56747 57529 - ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 + erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A) Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1797370 1798152 - ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia
--- a/test-data/output_mrsa.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_mrsa.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,9 +0,0 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT -MRSA0252.fna gi|49482253|ref|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 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 mecA_6 1-2007/2007 =============== 0/0 100.00 100.00 resfinder BX571856 mecA_6 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 56747 57529 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1797370 1798152 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1913785 1914672 blaZ_78 1-888/888 =============== 0/0 100.00 99.66 resfinder KU607301 blaZ_78 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 fosD_1 1-420/420 =============== 0/0 100.00 79.05 resfinder KC989517 fosD_1
--- a/test-data/output_noheader.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_noheader.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,8 +1,8 @@ -MRSA0252.fna gi|49482253|ref|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 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 mecA_6 1-2007/2007 =============== 0/0 100.00 100.00 resfinder BX571856 mecA_6 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 56747 57529 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A)_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1797370 1798152 ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia_1 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 1913785 1914672 blaZ_78 1-888/888 =============== 0/0 100.00 99.66 resfinder KU607301 blaZ_78 -MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 fosD_1 1-420/420 =============== 0/0 100.00 79.05 resfinder KC989517 fosD_1 +MRSA0252.fna gi|49482253|ref|NC_002952.2| 40786 41556 - aadD_1 1-771/771 =============== 0/0 100.00 99.74 resfinder AF181950 aadD Amikacin;Tobramycin +MRSA0252.fna gi|49482253|ref|NC_002952.2| 44919 46925 - mecA_6 1-2007/2007 =============== 0/0 100.00 100.00 resfinder BX571856 mecA Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam +MRSA0252.fna gi|49482253|ref|NC_002952.2| 55890 56621 + erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A) Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S +MRSA0252.fna gi|49482253|ref|NC_002952.2| 56747 57529 - ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1796513 1797244 + erm(A)_1 1-732/732 =============== 0/0 100.00 100.00 resfinder X03216 erm(A) Erythromycin;Lincomycin;Clindamycin;Quinupristin;Pristinamycin_IA;Virginiamycin_S +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1797370 1798152 - ant(9)-Ia_1 1-783/783 =============== 0/0 100.00 100.00 resfinder X02588 ant(9)-Ia +MRSA0252.fna gi|49482253|ref|NC_002952.2| 1913785 1914672 + blaZ_78 1-888/888 =============== 0/0 100.00 99.66 resfinder KU607301 blaZ Amoxicillin;Ampicillin;Penicillin;Piperacillin +MRSA0252.fna gi|49482253|ref|NC_002952.2| 2488459 2488878 + fosD_1 1-420/420 =============== 0/0 100.00 79.05 resfinder KC989517 fosD Fosfomycin
--- a/test-data/output_noresults.txt Mon Oct 07 14:57:31 2019 -0400 +++ b/test-data/output_noresults.txt Tue Oct 29 19:24:59 2019 -0400 @@ -1,1 +1,1 @@ -#FILE SEQUENCE START END GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT +#FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE