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4
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1 #!/usr/bin/env python3
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2 ''' configuration file to set up the paths and constants '''
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3 import os
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4
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5 MAIN_GIT_DIR = os.path.dirname(os.path.realpath(__file__))
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7
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6 TOOL_DATA = os.path.join(MAIN_GIT_DIR, "tool-data")
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4
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7 TMP = "tmp"
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10
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8 SC_MATRIX_SKELETON = os.path.join(TOOL_DATA, "{}.txt.sample")
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4
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9 AMBIGUOUS_TAG = "Ambiguous_domain"
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10 ## IO
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11 CLASS_FILE = "ALL.classification-new"
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12 LAST_DB_FILE = "ALL_protein-domains_05.fasta"
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13 DOM_PROT_SEQ = "dom_prot_seq.fa"
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14 FILT_DOM_GFF = "domains_filtered.gff"
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15 EXTRACT_DOM_STAT = "domains_counts.txt"
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16 EXTRACT_OUT_DIR = "extracted_domains"
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9
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17 FASTA_LINE = 60
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18 SOURCE_PROFREP = "profrep"
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19 SOURCE_DANTE = "dante"
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20 DOMAINS_FEATURE = "protein_domain"
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21 PHASE = "."
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22 HEADER_GFF = "##gff-version 3"
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23 DOMAINS_GFF = "output_domains.gff"
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