# Validation to use for good commands from now on
validation: | sortseq_tools validate -t dataset

# Test use of tags
good: sortseq_tools preprocess -i files_good_tags.txt --tagkey tagkey_good_usethis.txt
bad:  sortseq_tools preprocess -i files_good_tags_someunknown.txt --tagkey tagkey_good_usethis.txt
bad:  sortseq_tools preprocess -i files_good_tags.txt --tagkey tagkey_bad_badseqcol.txt
bad:  sortseq_tools preprocess -i files_bad_tags_variablelength.txt --tagkey tagkey_good_usethis.txt
bad:  sortseq_tools preprocess -i files_bad_tags_rnacol.txt --tagkey tagkey_good_usethis.txt
bad:  sortseq_tools preprocess -i files_bad_tags_rnachars.txt --tagkey tagkey_good_usethis.txt

# seqtype option is applied properly
good: sortseq_tools preprocess -i files_good.txt 
good: sortseq_tools preprocess -i files_good.txt --seqtype=dna
bad:  sortseq_tools preprocess -i files_good.txt --seqtype=rna
bad:  sortseq_tools preprocess -i files_good.txt --seqtype=protein
bad:  sortseq_tools preprocess -i files_good_rna.txt --seqtype=dna
good: sortseq_tools preprocess -i files_good_rna.txt --seqtype=rna
bad:  sortseq_tools preprocess -i files_good_rna.txt --seqtype=protein
bad:  sortseq_tools preprocess -i files_good_pro.txt --seqtype=dna
bad:  sortseq_tools preprocess -i files_good_pro.txt --seqtype=rna
good: sortseq_tools preprocess -i files_good_pro.txt --seqtype=protein

# fasta files are processed properly
good: sortseq_tools preprocess -i files_good_fasta.txt --seqtype=dna
bad:  sortseq_tools preprocess -i files_good_fasta.txt --seqtype=rna
bad:  sortseq_tools preprocess -i files_good_fasta.txt
good: sortseq_tools preprocess -i files_good_fasta.txt --seqtype=protein

# mix of formats
good: sortseq_tools preprocess -i files_good_mixofdnaformats.txt --seqtype=dna
bad:  sortseq_tools preprocess -i files_good_mixofdnaformats.txt --seqtype=rna
bad:  sortseq_tools preprocess -i files_good_mixofdnaformats.txt --seqtype=protein
bad:  sortseq_tools preprocess -i files_good_mixofdnaformats.txt

# Variations within good files are tolerated
good: sortseq_tools preprocess -i files_good_comments.txt
good: sortseq_tools preprocess -i files_good_nonconsecutivebins.txt
good: sortseq_tools preprocess -i files_good_samefile.txt

bad:  sortseq_tools preprocess -i files_bad_badcols.txt
bad:  sortseq_tools preprocess -i files_bad_extracol.txt
bad:  sortseq_tools preprocess -i files_bad_nofiles.txt
bad:  sortseq_tools preprocess -i files_bad_nonintegerbins.txt
bad:  sortseq_tools preprocess -i files_bad_nonuniquebins.txt
bad:  sortseq_tools preprocess -i files_badio_nonexistentfile.txt
bad:  sortseq_tools preprocess -i files_badtype_dnaandprotein.txt
bad:  sortseq_tools preprocess -i files_badtype_dnaandrna.txt
bad:  sortseq_tools preprocess -i files_badtype_rnaandprotein.txt