Appreciate @AdmiralenOla if you could guide me in making the approproate traits file for scoary.
scoary seems to read the gene presence absence file accurately.
Command: /home/svu/e0512807/miniconda3/envs/scoary/bin/scoary -t traits_scoary_plant_soil.tsv -g matrix_scoary_plant_soil.tsv --no_pairwise -c BH -p 1.0
Performing no pairwise comparisons. Ignoring all tree related options (user tree, population aware-correction, permutations).
Reading gene presence absence file
Ignoring relatedness among input sample and performing only population structure-naive analysis.
Reading traits file
Traceback (most recent call last):
File "/home/svu/e0512807/miniconda3/envs/scoary/bin/scoary", line 10, in
sys.exit(main())
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 268, in main
strains)
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 551, in Csv_to_dic
tab = list(zip(*csv.reader(csvfile, delimiter=delimiter)))
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0x82 in position 10: ordinal not in range(128)
Appreciate @AdmiralenOla if you could guide me in making the approproate traits file for scoary. scoary seems to read the gene presence absence file accurately.
Command: /home/svu/e0512807/miniconda3/envs/scoary/bin/scoary -t traits_scoary_plant_soil.tsv -g matrix_scoary_plant_soil.tsv --no_pairwise -c BH -p 1.0 Performing no pairwise comparisons. Ignoring all tree related options (user tree, population aware-correction, permutations). Reading gene presence absence file Ignoring relatedness among input sample and performing only population structure-naive analysis. Reading traits file Traceback (most recent call last): File "/home/svu/e0512807/miniconda3/envs/scoary/bin/scoary", line 10, in
sys.exit(main())
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 268, in main
strains)
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/site-packages/scoary/methods.py", line 551, in Csv_to_dic
tab = list(zip(*csv.reader(csvfile, delimiter=delimiter)))
File "/home/svu/e0512807/miniconda3/envs/scoary/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0x82 in position 10: ordinal not in range(128)