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add example data and increase travis perl to 5.24
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| # Example dataset | ||
| In the input_data subdirectory there are 3 published Salmonella genomes from different STs. A snapshot of the Salmonella MLST database is in this subdirectory. | ||
|
|
||
| ``` | ||
| cd example | ||
| export MLST_DATABASES=./mlst_databases | ||
| get_sequence_type -c -s 'Salmonella enterica' input_data/*.fa | ||
| ``` | ||
|
|
||
| The expected output files are located in the expected_output_data directory. Each of the 3 genomes has been assigned an ST and there is a file with the sequences of the alleles concatenated. This can then be used as input to RAxML to produce a basic phylogenetic tree. |
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| >Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1/1-3336 | ||
| GTTTTTCGCCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTAC | ||
| CGCGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATC | ||
| GCCAAGAAATACTTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATG | ||
| GGCGACATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGC | ||
| CCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGT | ||
| GACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAA | ||
| CCGGTATTTGACCGACTGGATGCGGACATCGCCCATGCGCTGATGAGCATCAATGCGGTG | ||
| AAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGC | ||
| GATGAAATCACGGCGCAGGGTATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCAT | ||
| GAGCCAGGCGCCACTACCGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCG | ||
| GAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGT | ||
| AGCCGCTTCTCGCTGTCTACGCTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAA | ||
| AGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAG | ||
| TTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAA | ||
| GGTAGCGAACTGCGCACTGTTGCGACCGACGGCCACCGTCTGGCGGTGTGCTCAATGCCG | ||
| CTGGAGGCGTCTTTACCTAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTG | ||
| ATGCGTATGCTCGACGGTGGCGAAAACCCGCTGCGCGTGCAGGCAACGCTGACGGAAAAC | ||
| GATCTGGTTTTTGCCCTTTCACAGCACTCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGG | ||
| GATGGACGAAACTGGCCTGCGTCGCCGCGCTATTTCTCGATTGGCCGCACCACGGCGCTC | ||
| GCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAA | ||
| GCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGT | ||
| GGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGTTCGCGGAGCCGAAGTCAGT | ||
| TTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGC | ||
| TGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAAATTGCG | ||
| GGATGCCAGAAGGTGGTTCTGTGCTCGCCGCCACCCATCGCTGATGAAATCCTCTATGCG | ||
| GCGCAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCT | ||
| CTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCC | ||
| TTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATG | ||
| CCAGCCGGGCCGTCTGAAGTGCTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTC | ||
| GCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACG | ||
| CCGGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTG | ||
| CCGCGCGCGGGCACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGAT | ||
| TTAGCGCAGTGCGTCAGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATT | ||
| CTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCCCATCGCACCCCCGATAAACTGTTC | ||
| AGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGC | ||
| GCGGCACACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCG | ||
| GTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGC | ||
| GGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGGGCGGCGAACGCCGCACTGCTG | ||
| GCAGCGCAAATTTTGGCTACGCATGATAGCGCGCTGCATCGGCGCATCGCCGACAAACGC | ||
| TTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCG | ||
| GGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCTATGCTGAAAGAGATG | ||
| GTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGT | ||
| CGTCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAGTTT | ||
| GCCGGTAAACATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCG | ||
| TCAGATATCGAAACTGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCAT | ||
| CTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACCGACTGGAC | ||
| GAACCGAGCAGTAATAAAGTGCTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGC | ||
| CAGGGCGTGGTTCAGGTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCC | ||
| GCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGT | ||
| GACCCGCGCCAGGTGCCGGACGCCAGGCTGTTGAAATCGATGTCCTACCAGGAAGCGATG | ||
| GAGCTCTCTTACTTCGGCGCTAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAG | ||
| TTCCAGATCCCCTGTCTGATTAAAAATACCGGCAATCCGCAGGCGCCAGGAACGCTGATC | ||
| GGCGCGTCCAGCGACGATGATAATCTGCCGGTTAAAGGGATCTCTAACCTTAACAACATG | ||
| GCGATGTTTAGCGTCTCCGGCCCGGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTT | ||
| TTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAG | ||
| TACAGCATCAGCTTCTGTGTGCCGCAGAGTGACTGC | ||
| >Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1/1-3336 | ||
| gtttttcgtccgggacacgcggattacacctatgagcagaaatacggcctgcgcgattac | ||
| cgtggcggtggacgttcttccgcgcgtgaaaccgcgatgcgcgtagcggcaggggcgatc | ||
| gccaagaaatacctggcggaaaagttcggcatcgaaatccgcggctgcctgacccagatg | ||
| ggcgacattccgctggagattaaagactggcgtcaggttgagcttaatccgttcttttgt | ||
| cccgatgcggacaaacttgacgcgctggacgaactgatgcgcgcgctgaaaaaagagggt | ||
| gactccatcggcgcgaaagtgacggtgatggcgagcggcgtgccggcagggcttggcgaa | ||
| ccggtatttgaccgactggatgcggacatcgcccatgcgctgatgagcattaatgcggtg | ||
| aaaggcgtggagatcggcgaaggatttaacgtggtggcgctgcgcggcagccagaatcgc | ||
| gatgaaatcacggcgcagggtatggagatggtcgcgcgcgttacgctttctcagccgcat | ||
| gagccaggcgccactaccgtgccggcgcggaaattctttgatatctgccgcggcctgccg | ||
| gagggcgcggagattgccgttcagttggaaggcgatcggatgctggtgcgttctggccgt | ||
| agccgcttctcgctgtctacgctgcctgccgccgatttcccgaatcttgacgactggcaa | ||
| agcgaagttgaatttacgctgccgcaggccacgatgaagcgcctgattgaatcgacccag | ||
| ttttcgatggcccatcaggatgtgcgctactacttaaacggtatgctgtttgaaacggaa | ||
| ggtagcgaactgcgcactgtcgcgaccgacggccaccgtctggcggtgtgctcaatgccg | ||
| ctggaagcgtctttacccagccactcggtgattgtgccgcgtaaaggcgtgattgaactg | ||
| atgcgtatgctcgacggcggcgaaaacccgctgcgcgtgcaggcgacgctgacggaaaac | ||
| gatctggtttttgccctttcacagcacgctgtcgcctttgctcacgcccagctccagcgg | ||
| gatggtcgaaactggcctgtggcgccgcgctatttcgcgattggccgcaccacggcgctc | ||
| gcccttcataccgttagcgggttcgatattcgttatccattggatcgggaaatcagcgaa | ||
| gccttgctacaattacctgaattacaaaatattgcgggcaaacgcgcgctgattttgcgt | ||
| ggcaatggcggccgcgaactgctgggcgaaaccctgacagcgcgcggagccgaagtcagt | ||
| ttttgtgaatgttatcaacgatgtgcgaaacattacgatggcgcggaagaagcgatgcgc | ||
| tggcatactcgcggcgtaacaacgcttgttgttaccagcggcgagatgttgcaaattgcg | ||
| ggatgccagaaggtggttctgtgctcgccgccgcccatcgctgatgaaatcctctatgcg | ||
| gcgcaactgtgtggcgtgcaggaaatctttaacgtcggcggcgcgcaggcgattgccgct | ||
| ctggccttcggcagcgagtccgtaccgaaagtggataaaatttttggccccggcaacgcc | ||
| tttgtaaccgaagccaaacgtcaggtcagccagcgtctcgacggcgcggctatcgatatg | ||
| ccagccgggccgtctgaagtactggtgatcgcagacagcggcgcaacaccggatttcgtc | ||
| gcttctgacctgctctcccaggctgagcacggcccggattcccaggtgatcctgctgacg | ||
| cctgatgctgacattgcccgcaaggtggcggaggcggtagaacgtcaactggcggaactg | ||
| ccgcgcgcggacaccgcccggcaggccctgagcgccagtcgtctgattgtgaccaaagat | ||
| ttagcgcagtgcgtcagcgactgggctaccatgcaattcgccgccgaaatttttgaaatt | ||
| ctggatgtcccgcaccatgtagaagtggtttccgctcatcgcacccccgataaactgttc | ||
| agcttcgccgaaacggcggaagagaacggatatcaagtgattattgccggcgcgggcggc | ||
| gcggcgcacctgccgggaatgattgcggcaaaaacgctggtcccggtactcggcgtgccg | ||
| gtacaaagcgctgcgctaagcggcgtggatagcctctactccatcgtgcagatgccgcgc | ||
| ggcattccggtgggtacgctggcgatcggtaaagccggtgccgctaacgccgccctgctc | ||
| gccgcgcagattctggcgcaacacgacgcggaactgcatcagcgcattgccgacaaacgc | ||
| ttcctgaacgaactgaccgccgctgaagggctggaacgttatctgggcgccaaattcccg | ||
| ggtgcgaaacgtttctcgctcgaggggggagatgcgctgatacccatgctgaaagagatg | ||
| gttcgccatgcgggtaacagcggcactcgcgaagtggtgctggggatggcgcaccgcggt | ||
| cgcctgaacgtgctgatcaacgtactgggtaaaaaaccgcaggatctgttcgacgaattt | ||
| gccggtaagcataaagaacatctgggtaccggcgacgtgaagtatcacatgggcttctcg | ||
| tcagatatcgaaaccgaaggcggtctggttcacctggcgctggcgtttaacccatcgcat | ||
| ctggaaattgtgagcccggtggtgatgggctccgtgcgcgcccgtctggacagactggac | ||
| gaaccgagcagcaacaaagtgttgccgatcactattcacggcgacgccgcggtgaccggc | ||
| cagggcgtggttcaggtgctgggccgtaatggttccgactattccgccgccgtgctggcc | ||
| gcctgtttacgcgctgactgctgtgaaatctggactgacgtcgatggcgtgtatacctgt | ||
| gacccgcgccaggtgccggacgccaggctgctgaaatcgatgtcctaccaggaagcgatg | ||
| gaactctcttacttcggcgccaaagtccttcaccctcgcaccattacgcccatcgcccag | ||
| ttccagatcccctgtctgattaaaaataccggtaatccgcaggcgccaggaacgctgatc | ||
| ggcgcgtccagcgacgatgataacctgccggttaaagggatctctaaccttaacaacatg | ||
| gcgatgtttagcgtctccggcccgggaatgaaagggatgattgggatggcggcgcgtgtt | ||
| ttcgccgccatgtctcgcgccgggatctcggtggtgctcattacccagtcctcctctgag | ||
| tacagcatcagtttctgtgtgccgcagagtgactgc | ||
| >Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2/1-3336 | ||
| GTTTTTCGTCCGGGACACGCGGATTACACCTATGAGCAGAAATACGGCCTGCGCGATTAC | ||
| CGTGGCGGTGGACGTTCTTCCGCGCGTGAAACCGCGATGCGCGTAGCGGCAGGGGCGATC | ||
| GCCAAGAAATACCTGGCGGAAAAGTTCGGCATCGAAATCCGCGGCTGCCTGACCCAGATG | ||
| GGCGATATTCCGCTGGAGATTAAAGACTGGCGTCAGGTTGAGCTTAATCCGTTCTTTTGT | ||
| CCCGATGCGGACAAACTTGACGCGCTGGACGAACTGATGCGCGCGCTGAAAAAAGAGGGC | ||
| GACTCCATCGGCGCGAAAGTGACGGTGATGGCGAGCGGCGTGCCGGCAGGGCTTGGCGAA | ||
| CCGGTATTTGACCGACTGGATGCGGACATTGCCCATGCGCTGATGAGCATCAATGCGGTG | ||
| AAAGGCGTGGAGATCGGCGAAGGATTTAACGTGGTGGCGCTGCGCGGCAGCCAGAATCGC | ||
| GATGAAATCACGGCGCAGGGTATGGAGATGGTCGCGCGCGTTACGCTTTCTCAGCCGCAT | ||
| GAGCCGGGTGCTACTACTGTGCCGGCGCGGAAATTCTTTGATATCTGCCGCGGCCTGCCG | ||
| GAGGGCGCGGAGATTGCCGTTCAGTTGGAAGGCGATCGGATGCTGGTGCGTTCTGGCCGT | ||
| AGCCGCTTCTCGCTGTCTACACTGCCTGCCGCCGATTTCCCGAATCTTGACGACTGGCAA | ||
| AGCGAAGTTGAATTTACGCTGCCGCAGGCCACGATGAAGCGCCTGATTGAAGCGACCCAG | ||
| TTTTCGATGGCCCATCAGGATGTGCGCTACTACTTAAACGGTATGCTGTTTGAAACGGAA | ||
| GGTAGCGAACTGCGCACTGTCGCGACCGACGGCCACCGCCTGGCGGTGTGCTCAATGCCG | ||
| CTGGAAGCGTCTTTACCCAGCCACTCGGTGATTGTGCCGCGTAAAGGCGTGATTGAACTG | ||
| ATGCGTATGCTCGACGGCGGCGAAAACCCGCTGCGCGTGCAGGCGACTCTGACGGAAAAC | ||
| GATCTGGTTTTTGCCCTTTCACAGCACGCCGTCGCCTTTGCTCACGCCCAGCTCCAGCGG | ||
| GATGGTCGAAACTGGCCTGCGTCGCCGCGCTATTTCGCGATTGGCCGCACCACGGCGCTC | ||
| GCCCTTCATACCGTTAGCGGGTTCGATATTCGTTATCCATTGGATCGGGAAATCAGCGAA | ||
| GCCTTGCTACAATTACCTGAATTACAAAATATTGCGGGCAAACGCGCGCTGATTTTGCGT | ||
| GGCAATGGCGGCCGCGAACTGCTGGGCGAAACCCTGACAGCTCGCGGAGCCGAAGTCAGT | ||
| TTTTGTGAATGTTATCAACGATGTGCGAAACATTACGATGGCGCGGAAGAAGCGATGCGC | ||
| TGGCATACTCGCGGCGTAACAACGCTTGTTGTTACCAGCGGCGAGATGTTGCAAATTGCG | ||
| GGATGTCAGAACGTGGTTCTGTGCTCGCCGCCGCCCATCGCTGATGAAATCCTCTATGCG | ||
| GCACAACTGTGTGGCGTGCAGGAAATCTTTAACGTCGGCGGCGCGCAGGCGATTGCCGCT | ||
| CTGGCCTTCGGCAGCGAGTCCGTACCGAAAGTGGATAAAATTTTTGGCCCCGGCAACGCC | ||
| TTTGTAACCGAAGCCAAGCGTCAGGTCAGCCAGCGTCTCGACGGCGCGGCTATCGATATG | ||
| CCAGCCGGGCCGTCTGAAGTACTGGTGATCGCCGACAGCGGCGCAACACCGGATTTCGTC | ||
| GCTTCTGACCTGCTCTCCCAGGCTGAGCACGGCCCGGATTCCCAGGTGATCCTGCTGACG | ||
| CCTGATGCTGACATTGCCCGCAAGGTGGCGGAGGCGGTAGAACGTCAACTGGCGGAACTG | ||
| CCGCGCGCGGACACCGCCCGGCAGGCCCTGAGCGCCAGTCGTCTGATTGTGACCAAAGAT | ||
| TTAGCGCAGTGCGTCAGCGACTGGGCTACCATGCAATTCGCCGCCGAAATTTTTGAAATT | ||
| CTGGATGTCCCGCACCATGTAGAAGTGGTTTCCGCTCATCGCACCCCCGATAAACTGTTC | ||
| AGCTTCGCCGAAACGGCGGAAGAGAACGGATATCAAGTGATTATTGCCGGCGCGGGCGGC | ||
| GCGGCGCACCTGCCGGGAATGATTGCGGCAAAAACGCTGGTCCCGGTACTCGGCGTGCCG | ||
| GTACAAAGCGCTGCGCTCAGCGGCGTGGATAGCCTCTACTCCATCGTGCAGATGCCGCGC | ||
| GGCATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTC | ||
| GCCGCGCAGATTCTGGCGCAACACGACGCGGAACTGCATCAGCGCATCGCTGACAAACGC | ||
| TTCCTGAACGAACTGACCGCCGCTGAAGGGCTGGAACGTTATCTGGGCGCCAAATTCCCG | ||
| GGTGCGAAACGTTTCTCGCTCGAGGGGGGAGATGCGCTGATACCCATGCTGAAAGAGATG | ||
| GTTCGCCATGCGGGTAACAGCGGCACTCGCGAAGTGGTGCTGGGGATGGCGCACCGCGGT | ||
| CGCCTGAACGTGCTGATCAACGTACTGGGTAAAAAACCGCAGGATCTGTTCGACGAATTT | ||
| GCCGGTAAGCATAAAGAACATCTGGGTACCGGCGACGTGAAGTATCACATGGGCTTCTCG | ||
| TCAGATATCGAAACCGAAGGCGGTCTGGTTCACCTGGCGCTGGCGTTTAACCCATCGCAT | ||
| CTGGAAATTGTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGAC | ||
| GAACCGAGCAGCAACAAAGTGTTGCCGATCACTATTCACGGCGACGCCGCGGTGACCGGC | ||
| CAGGGCGTGGTTCAGGTGCTGGGCCGTAATGGTTCCGACTATTCCGCCGCCGTGCTGGCC | ||
| GCCTGTTTACGCGCTGACTGCTGTGAAATCTGGACTGACGTCGATGGCGTGTATACCTGT | ||
| GACCCGCGTCAGGTGCCGGACGCCAGGCTGCTGAAATCGATGTCCTACCAGGAAGCGATG | ||
| GAACTCTCTTACTTCGGCGCCAAAGTCCTTCACCCTCGCACCATAACGCCTATCGCCCAG | ||
| TTCCAGATCCCCTGTCTGATTAAAAATACCGGTAATCCGCAGGCGCCAGGAACGCTGATC | ||
| GGCGCGTCCAGCGACGATGATAATCTGCCGGTGAAAGGGATCTCTAACCTTAACAACATG | ||
| GCGATGTTTAGCGTCTCCGGCCCTGGAATGAAAGGGATGATTGGGATGGCGGCGCGTGTT | ||
| TTCGCCGCCATGTCTCGCGCCGGGATCTCGGTGGTGCTCATTACCCAGTCCTCCTCTGAG | ||
| TACAGCATCAGTTTCTGTGTGCCGCAGAGTGACTGC |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,4 @@ | ||
| "Isolate" "ST" "New ST" "Contamination" "aroC" "dnaN" "hemD" "hisD" "purE" "sucA" "thrA" | ||
| "Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1" "2" "" "" "1" "1" "2" "1" "1" "1" "5" | ||
| "Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1" "19" "" "" "10" "7" "12" "9" "5" "9" "2" | ||
| "Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2" "365" "" "" "130" "97" "25" "125" "84" "9" "101" |
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