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DOGMA
DOGMA
Commit 647e1790 authored by Elias Dohmen's avatar Elias Dohmen
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fix dicots-eudicots

parent 82592c13
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Showing with 3 additions and 3 deletions
UserManual.pdf
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dogma.py
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......@@ -284,7 +284,7 @@ def score_single_transcriptome(annotation_file, outfile=None, max_dom_tup_len=3,
script_path = dirname(realpath(sys.argv[0]))
at = annotype
if hq_transcriptomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea', 'arthropods', 'dicots', 'fungi', 'monocots', 'plants', 'vertebrates'):
if hq_transcriptomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea', 'arthropods', 'eudicots', 'fungi', 'monocots', 'plants', 'vertebrates'):
hq_doms_path_list = [ospjoin(script_path, 'pfam' + pfam, 'reference-sets', hq_transcriptomes, filename) for
filename in
listdir(ospjoin(script_path, 'pfam' + pfam, 'reference-sets', hq_transcriptomes)) if
......@@ -363,7 +363,7 @@ def score_single_proteome(annotation_file, outfile=None, cutoff=2,
script_path = dirname(realpath(sys.argv[0]))
at = annotype
if hq_proteomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea', 'arthropods', 'dicots', 'fungi', 'monocots', 'plants', 'vertebrates'):
if hq_proteomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea', 'arthropods', 'eudicots', 'fungi', 'monocots', 'plants', 'vertebrates'):
hq_doms_path_list = [ospjoin(script_path, 'pfam' + pfam, 'reference-sets', hq_proteomes, filename) for
filename in listdir(ospjoin(script_path, 'pfam' + pfam, 'reference-sets', hq_proteomes)) if
(isfile(ospjoin(script_path, 'pfam' + pfam, 'reference-sets', hq_proteomes, filename)) and
......@@ -618,7 +618,7 @@ class SpeciesComparer(dict):
self.default_path = (ospjoin(self.script_path, 'reference-sets', 'archaea'),
ospjoin(self.script_path, 'reference-sets', 'arthropods'),
ospjoin(self.script_path, 'reference-sets', 'bacteria'),
ospjoin(self.script_path, 'reference-sets', 'dicots'),
ospjoin(self.script_path, 'reference-sets', 'eudicots'),
ospjoin(self.script_path, 'reference-sets', 'eukaryotes'),
ospjoin(self.script_path, 'reference-sets', 'fungi'),
ospjoin(self.script_path, 'reference-sets', 'insects'),
......
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