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fix extra tests
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Sara Sjunnebo committed Jan 23, 2018
1 parent bdc072e commit ae7ac49
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Showing 3 changed files with 9 additions and 9 deletions.
2 changes: 1 addition & 1 deletion t/Bio/Roary/CommandLine/Roary.t
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Expand Up @@ -67,7 +67,7 @@ SKIP:
);

my @keys = keys %{ $seq_len->sequence_lengths };
is( $seq_len->sequence_lengths->{ $keys[0] }, 65283, 'length of first sequence' );
is( $seq_len->sequence_lengths->{ $keys[0] }, 64983, 'length of first sequence' );

ok( -e 'core_alignment_header.embl', 'Core gene alignment header exists' );

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8 changes: 4 additions & 4 deletions t/data/real_data_1.gff
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
##sequence-region ERS111111|SC|contig000020 1 92255
ERS111111|SC|contig000020 Prodigal:2.60 CDS 241 921 . - 0 ID=11111_1#11_04055;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145956.2,protein motif:Pfam:PF07108.5;locus_tag=11111_1#11_04055;product=pathogenicity island-encoded protein A,PipA protein;protein_id=gnl|SC|11111_1#11_04055
ERS111111|SC|contig000020 Prodigal:2.60 CDS 1144 2019 . - 0 ID=11111_1#11_04056;gene=pipB2_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145957.1,similar to AA sequence:UniProtKB:Q8ZMM8,protein motif:CLUSTERS:PRK15197,protein motif:Cdd:COG5351,protein motif:Pfam:PF00805.16;locus_tag=11111_1#11_04056;product=secreted effector protein,Type III effector pipB2,secreted effector protein PipB,Uncharacterized protein conserved in bacteria,Pentapeptide repeats (8 copies);protein_id=gnl|SC|11111_1#11_04056
ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2237 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI
ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2156 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI
ERS111111|SC|contig000020 Prodigal:2.60 CDS 2567 2908 . - 0 ID=11111_1#11_04058;gene=sigE;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145959.1,similar to AA sequence:UniProtKB:O30917,protein motif:CLUSTERS:PRK15202,protein motif:Pfam:PF07824.6;locus_tag=11111_1#11_04058;product=chaperone protein SigE,Chaperone protein sigE,type III secretion chaperone protein SigE,Type III secretion chaperone domain;protein_id=gnl|SC|11111_1#11_04058
ERS111111|SC|contig000020 Prodigal:2.60 CDS 2925 4610 . - 0 ID=11111_1#11_04059;eC_number=3.1.3.-,3.1.3.-;gene=sopB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145960.1,similar to AA sequence:UniProtKB:O30916,protein motif:CLUSTERS:PRK15378,protein motif:Pfam:PF05925.6;locus_tag=11111_1#11_04059;product=inositol phosphate phosphatase SopB,Inositol phosphate phosphatase sopB,inositol phosphate phosphatase SopB,Enterobacterial virulence protein IpgD;protein_id=gnl|SC|11111_1#11_04059
ERS111111|SC|contig000020 Prodigal:2.60 CDS 5332 6801 . - 0 ID=11111_1#11_04060;eC_number=3.4.-.-;gene=pepD_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002215025.1,similar to AA sequence:UniProtKB:Q8G6Z9,protein motif:Pfam:PF03577.9;locus_tag=11111_1#11_04060;product=peptidase family C69,Dipeptidase,Peptidase family C69;protein_id=gnl|SC|11111_1#11_04060
Expand Down Expand Up @@ -47,7 +47,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 43804 44946 . + 0 ID=11111_1#11_0409
ERS111111|SC|contig000020 Prodigal:2.60 CDS 44992 45684 . + 0 ID=11111_1#11_04099;gene=yiiy;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216068.1,similar to AA sequence:UniProtKB:Q934G3,protein motif:CLUSTERS:PRK09980,protein motif:Cdd:COG3203,protein motif:Pfam:PF06178.7;locus_tag=11111_1#11_04099;product=outer membrane protein,Oligogalacturonate-specific porin kdgM precursor,outer membrane porin L,Outer membrane protein (porin),Oligogalacturonate-specific porin protein (KdgM);protein_id=gnl|SC|11111_1#11_04099
ERS111111|SC|contig000020 Prodigal:2.60 CDS 45967 47247 . + 0 ID=11111_1#11_04100;gene=nanT_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570893.1,similar to AA sequence:UniProtKB:P41036,protein motif:CLUSTERS:PRK12307,protein motif:Cdd:COG2814,protein motif:TIGRFAMs:TIGR00891,protein motif:Pfam:PF00083.18;locus_tag=11111_1#11_04100;product=putative sialic acid transporter,Sialic acid permease,putative sialic acid transporter,Arabinose efflux permease,MFS transporter%2C sialate:H+ symporter (SHS) family,Sugar (and other) transporter;protein_id=gnl|SC|11111_1#11_04100
ERS111111|SC|contig000020 Prodigal:2.60 CDS 47261 48364 . + 0 ID=11111_1#11_04101;eC_number=1.1.1.292;gene=yjhC;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216069.1,similar to AA sequence:UniProtKB:Q2I8V6,protein motif:CLUSTERS:PRK11579,protein motif:Pfam:PF01408.16;locus_tag=11111_1#11_04101;product=dehydrogenase-like protein,1%2C5-anhydro-D-fructose reductase,putative oxidoreductase,Oxidoreductase family%2C NAD-binding Rossmann fold;protein_id=gnl|SC|11111_1#11_04101
ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48788 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga)
ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48718 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga)
ERS111111|SC|contig000020 Prodigal:2.60 CDS 49024 49962 . + 0 ID=11111_1#11_04103;eC_number=1.1.1.79;gene=ghrA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729856.1,similar to AA sequence:UniProtKB:Q8ZQ30,protein motif:CLUSTERS:PRK15469,protein motif:Cdd:COG1932,protein motif:TIGRFAMs:TIGR01327,protein motif:Pfam:PF02826.13;locus_tag=11111_1#11_04103;product=2-hydroxyacid dehydrogenase,Glyoxylate/hydroxypyruvate reductase A,bifunctional glyoxylate/hydroxypyruvate reductase A,Phosphoserine aminotransferase,phosphoglycerate dehydrogenase,D-isomer specific 2-hydroxyacid dehydrogenase%2C NAD binding domain;protein_id=gnl|SC|11111_1#11_04103
ERS111111|SC|contig000020 Prodigal:2.60 CDS 50047 50784 . + 0 ID=11111_1#11_04104;eC_number=3.1.3.-;gene=ycdX;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570887.1,similar to AA sequence:UniProtKB:P75914,protein motif:CLUSTERS:PRK09248,protein motif:Cdd:COG1387,protein motif:TIGRFAMs:TIGR01856,protein motif:Pfam:PF02811.13;locus_tag=11111_1#11_04104;product=putative hydrolase,Probable phosphatase YcdX,putative hydrolase,Histidinol phosphatase and related hydrolases of the PHP family,histidinol phosphate phosphatase%2C HisJ family,PHP domain;protein_id=gnl|SC|11111_1#11_04104
ERS111111|SC|contig000020 Prodigal:2.60 CDS 50808 51362 . + 0 ID=11111_1#11_04105;gene=ycdY;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002146908.1,similar to AA sequence:UniProtKB:P75915,protein motif:CLUSTERS:PRK11621,protein motif:Cdd:COG3381,protein motif:Pfam:PF02613.9;locus_tag=11111_1#11_04105;product=chaperone%2C TorD family,Chaperone protein YcdY,twin-argninine leader-binding protein DmsD,Uncharacterized component of anaerobic dehydrogenases,Nitrate reductase delta subunit;protein_id=gnl|SC|11111_1#11_04105
Expand All @@ -72,7 +72,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 66575 67495 . - 0 ID=11111_1#11_0412
ERS111111|SC|contig000020 Prodigal:2.60 CDS 67715 68767 . + 0 ID=11111_1#11_04124;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087420.1,protein motif:CLUSTERS:PRK00142,protein motif:Cdd:COG2210,protein motif:Pfam:PF00581.14;locus_tag=11111_1#11_04124;product=Rhodanese-like sulfurtransferase,putative rhodanese-related sulfurtransferase,Uncharacterized conserved protein,Rhodanese-like domain;protein_id=gnl|SC|11111_1#11_04124
ERS111111|SC|contig000020 Prodigal:2.60 CDS 68819 69394 . - 0 ID=11111_1#11_04125;gene=yceI_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087865.1,similar to AA sequence:UniProtKB:P0A8X2,protein motif:CLUSTERS:PRK03757,protein motif:Cdd:COG2353,protein motif:Pfam:PF04264.7;locus_tag=11111_1#11_04125;product=YceI protein,hypothetical protein,hypothetical protein,Uncharacterized conserved protein,YceI-like domain;protein_id=gnl|SC|11111_1#11_04125
ERS111111|SC|contig000020 Prodigal:2.60 CDS 69391 69795 . - 0 ID=11111_1#11_04126;gene=yceJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_005212184.1,similar to AA sequence:UniProtKB:P75925,protein motif:CLUSTERS:PRK11513,protein motif:Pfam:PF00033.13;locus_tag=11111_1#11_04126;product=cytochrome b561-like protein 2,Cytochrome b561 homolog 2,cytochrome b561,Cytochrome b(N-terminal)/b6/petB;protein_id=gnl|SC|11111_1#11_04126
ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70339 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127
ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70243 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127
ERS111111|SC|contig000020 Prodigal:2.60 CDS 70380 71498 . - 0 ID=11111_1#11_04128;eC_number=1.5.3.1,1.5.3.-;gene=solA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729880.1,similar to AA sequence:UniProtKB:P40874,protein motif:CLUSTERS:PRK11259,protein motif:Cdd:COG4121,protein motif:TIGRFAMs:TIGR01377,protein motif:Pfam:PF01266.18;locus_tag=11111_1#11_04128;product=sarcosine oxidase,N-methyl-L-tryptophan oxidase,N-methyltryptophan oxidase,Uncharacterized conserved protein,sarcosine oxidase%2C monomeric form,FAD dependent oxidoreductase;protein_id=gnl|SC|11111_1#11_04128
ERS111111|SC|contig000020 Prodigal:2.60 CDS 71611 71865 . - 0 ID=11111_1#11_04129;gene=bssS;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570863.1,protein motif:CLUSTERS:PRK12301;locus_tag=11111_1#11_04129;product=biofilm formation regulatory protein BssS,biofilm formation regulatory protein BssS;protein_id=gnl|SC|11111_1#11_04129
ERS111111|SC|contig000020 Prodigal:2.60 CDS 72155 72418 . - 0 ID=11111_1#11_04130;gene=dinI_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729882.1,similar to AA sequence:UniProtKB:P0ABR1,protein motif:CLUSTERS:PRK10597,protein motif:Pfam:PF06183.7;locus_tag=11111_1#11_04130;product=damage-inducible protein,DNA-damage-inducible protein I,DNA damage-inducible protein I,DinI-like family;protein_id=gnl|SC|11111_1#11_04130
Expand All @@ -98,7 +98,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 87332 88429 . + 0 ID=11111_1#11_0414
ERS111111|SC|contig000020 Prodigal:2.60 CDS 88429 89379 . + 0 ID=11111_1#11_04150;eC_number=3.2.1.-;gene=flgJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729902.1,similar to AA sequence:UniProtKB:P15931,protein motif:CLUSTERS:PRK05684,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02541,protein motif:Pfam:PF01832.14;locus_tag=11111_1#11_04150;product=flagellar protein FlgJ,Peptidoglycan hydrolase flgJ,flagellar rod assembly protein/muramidase FlgJ,Rod binding protein,flagellar rod assembly protein/muramidase FlgJ,Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase;protein_id=gnl|SC|11111_1#11_04150
ERS111111|SC|contig000020 Prodigal:2.60 CDS 89444 91105 . + 0 ID=11111_1#11_04151;gene=flgK;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729903.1,similar to AA sequence:UniProtKB:P0A1J5,protein motif:CLUSTERS:PRK08147,protein motif:Cdd:COG1749,protein motif:TIGRFAMs:TIGR02492,protein motif:Pfam:PF06429.7;locus_tag=11111_1#11_04151;product=flagellar hook-associated protein 1,Flagellar hook-associated protein 1,flagellar hook-associated protein FlgK,Flagellar hook protein FlgE,flagellar hook-associated protein FlgK,Domain of unknown function (DUF1078);protein_id=gnl|SC|11111_1#11_04151
ERS111111|SC|contig000020 Prodigal:2.60 CDS 91120 92073 . + 0 ID=11111_1#11_04152;gene=flgL;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729904.1,similar to AA sequence:UniProtKB:P16326,protein motif:CLUSTERS:PRK08027,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02550,protein motif:Pfam:PF00669.14;locus_tag=11111_1#11_04152;product=flagellar hook-associated protein 3,Hook-filament junction protein,flagellar hook-associated protein FlgL,Rod binding protein,flagellar hook-associated protein 3,Bacterial flagellin N-terminal helical region;protein_id=gnl|SC|11111_1#11_04152
ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92255 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k
ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92179 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k
##FASTA
>ERS111111|SC|contig000020
TATCCGGGCAGCCCGTTTACGGGCCGTAAGTAACGAAGTTTGATGCAAATGTCAGATCGT
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