Mercurial > repos > greg > lrn_risk

comparison lrn_risk.py @ 4:8fe04662585c draft

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Uploaded
author greg
date Tue, 29 Aug 2023 01:23:22 +0000
parents 5a27ac020c9e
children 5aa8560d9d91
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3:5a27ac020c9e 4:8fe04662585c
80 80
81 81
82 def gene_dist(f, blast, gtdb): 82 def gene_dist(f, blast, gtdb):
83 # get within-species prevalence of genes 83 # get within-species prevalence of genes
84 # for virulence factors (VFs): uses VFDB VFs detected via ABRicate's VFDB db 84 # for virulence factors (VFs): uses VFDB VFs detected via ABRicate's VFDB db
85 # for AMR genes: uses AMR genes detected via ABRicate's ResFinder db 85 # for AMR genes: uses AMR genes detected via ABRicate + PIMA db
86 # for VFs and AMR genes: genes were detected via ABRicate XXX 86 # for VFs and AMR genes: genes were detected via ABRicate XXX
87 # minimum nucleotide identity and coverage values >=80% 87 # minimum nucleotide identity and coverage values >=80%
88 # total of 61,161 genomes queried 88 # total of 61,161 genomes queried
89 # takes VFDB or AMR gene distribution file as input (f) 89 # takes VFDB or AMR gene distribution file as input (f)
90 # BLAST file of VFDB or AMR genes (blast) 90 # BLAST file of VFDB or AMR genes (blast)
130 perc = items[4] 130 perc = items[4]
131 perc = str(round(float(perc), 2)) 131 perc = str(round(float(perc), 2))
132 ann = items[-1] 132 ann = items[-1]
133 freetext = '{0}/{1} ({2}%)'.format(pres, denom, perc) 133 freetext = '{0}/{1} ({2}%)'.format(pres, denom, perc)
134 elif gtdb != '(Unknown Species)': 134 elif gtdb != '(Unknown Species)':
135 ann = annd[key] 135 ann = 'NA'
136 denom = gtdbd[gtdb] 136 denom = gtdbd[gtdb]
137 freetext = "*WARNING" 137 freetext = "*WARNING"
138 warnings.append("*WARNING: This gene has never been detected in this species! Interpret with caution!") 138 warnings.append("*WARNING: This gene has never been detected in this species! Interpret with caution!")
139 else: 139 else:
140 ann = annd[key] 140 ann = 'NA'
141 freetext = "**WARNING" 141 freetext = "**WARNING"
142 warnings.append("**WARNING: This genome belongs to an undescribed species. Interpret with caution!") 142 warnings.append("**WARNING: This genome belongs to an undescribed species. Interpret with caution!")
143 finallines.append('%s\t%s\t%s' % (bv, ann, freetext)) 143 finallines.append('%s\t%s\t%s' % (bv, ann, freetext))
144 return [finallines, warnings] 144 return [finallines, warnings]
145 145