comparison lrn_risk.py @ 5:5aa8560d9d91 draft

Uploaded

4:8fe04662585c

                perc = str(round(float(perc), 2))
                ann = items[-1]
                freetext = '{0}/{1} ({2}%)'.format(pres, denom, perc)
            elif gtdb != '(Unknown Species)':
                ann = 'NA'
                denom = gtdbd[gtdb]
                freetext = "*WARNING"
                warnings.append("*WARNING: This gene has never been detected in this species! Interpret with caution!")
            else:
                ann = 'NA'
                freetext = "**WARNING"
                warnings.append("**WARNING: This genome belongs to an undescribed species. Interpret with caution!")
            finallines.append('%s\t%s\t%s' % (bv, ann, freetext))
    return [finallines, warnings]

5:5aa8560d9d91

                perc = str(round(float(perc), 2))
                ann = items[-1]
                freetext = '{0}/{1} ({2}%)'.format(pres, denom, perc)
            elif gtdb != '(Unknown Species)':
                ann = 'NA'
                if gtdb in gtdbd.keys():
                    denom = gtdbd[gtdb]
                else:
                    denom = 'NA' 
                freetext = "*WARNING"
                warnings.append("*WARNING: This gene has never been detected in this species and/or this species has not been included in the LRNRisk database! Interpret with caution!")
            else:
                ann = 'NA'
                denom = 'NA'
                freetext = "**WARNING"
                warnings.append("**WARNING: This genome belongs to an undescribed species. Interpret with caution!")
            finallines.append('%s\t%s\t%s' % (bv, ann, freetext))
    return [finallines, warnings]