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1 #!/usr/bin/env python
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2
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3 """
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4 Definitions for the ectyper project
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5 """
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6
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7 import os
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8
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9 ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
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10 DATA_DIR = os.path.join(ROOT_DIR, 'Data')
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11 WORKPLACE_DIR = os.getcwd()
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12
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13 SEROTYPE_FILE = os.path.join(DATA_DIR, 'ectyper_data.fasta')
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14 SEROTYPE_ALLELE_JSON = os.path.join(DATA_DIR, 'ectyper_dict.json')
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15 COMBINED = os.path.join(DATA_DIR, 'combined.fasta')
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16
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17 ECOLI_MARKERS = os.path.join(DATA_DIR, 'ecoli_specific_markers.fasta')
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18 SAMTOOLS = 'samtools'
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19 REFSEQ_SUMMARY = os.path.join(DATA_DIR, 'assembly_summary_refseq.txt')
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20 REFSEQ_SKETCH = os.path.join(DATA_DIR, 'refseq.genomes.k21s1000.msh')
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