Mercurial > repos > jpetteng > ectyper
comparison ecoli_serotyping/definitions.py @ 6:fe3ceb5c4214 draft
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| author | jpetteng |
|---|---|
| date | Fri, 05 Jan 2018 15:43:14 -0500 |
| parents | |
| children |
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| 5:a202cc394af8 | 6:fe3ceb5c4214 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 """ | |
| 4 Definitions for the ectyper project | |
| 5 """ | |
| 6 | |
| 7 import os | |
| 8 | |
| 9 ROOT_DIR = os.path.dirname(os.path.abspath(__file__)) | |
| 10 DATA_DIR = os.path.join(ROOT_DIR, 'Data') | |
| 11 WORKPLACE_DIR = os.getcwd() | |
| 12 | |
| 13 SEROTYPE_FILE = os.path.join(DATA_DIR, 'ectyper_data.fasta') | |
| 14 SEROTYPE_ALLELE_JSON = os.path.join(DATA_DIR, 'ectyper_dict.json') | |
| 15 COMBINED = os.path.join(DATA_DIR, 'combined.fasta') | |
| 16 | |
| 17 ECOLI_MARKERS = os.path.join(DATA_DIR, 'ecoli_specific_markers.fasta') | |
| 18 SAMTOOLS = 'samtools' | |
| 19 REFSEQ_SUMMARY = os.path.join(DATA_DIR, 'assembly_summary_refseq.txt') | |
| 20 REFSEQ_SKETCH = os.path.join(DATA_DIR, 'refseq.genomes.k21s1000.msh') |