--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoli_serotyping/definitions.py	Fri Jan 05 15:43:14 2018 -0500
@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+"""
+    Definitions for the ectyper project
+"""
+
+import os
+
+ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
+DATA_DIR = os.path.join(ROOT_DIR, 'Data')
+WORKPLACE_DIR = os.getcwd()
+
+SEROTYPE_FILE = os.path.join(DATA_DIR, 'ectyper_data.fasta')
+SEROTYPE_ALLELE_JSON = os.path.join(DATA_DIR, 'ectyper_dict.json')
+COMBINED = os.path.join(DATA_DIR, 'combined.fasta')
+
+ECOLI_MARKERS = os.path.join(DATA_DIR, 'ecoli_specific_markers.fasta')
+SAMTOOLS = 'samtools'
+REFSEQ_SUMMARY = os.path.join(DATA_DIR, 'assembly_summary_refseq.txt')
+REFSEQ_SKETCH = os.path.join(DATA_DIR, 'refseq.genomes.k21s1000.msh')