from qiime.plugins import phylogeny, alignment
from q2_types import FeatureData, AlignedSequence, Sequence
import qiime
aligned_seqs = qiime.Artifact.import_data(FeatureData[AlignedSequence], 'aligned-dna-sequences.fasta')
# standard error goes to terminal where "jupyter notebook" is running
tree = phylogeny.methods.fasttree(aligned_seqs)
print(tree.tree.uuid)
Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. Command: FastTree -nt /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/qiime2-archive-wto551o4/aa4ef5af-050a-4cfc-a768-4fe59484f8d6/data/aligned-dna-sequences.fasta 3f2db99e-ad89-4006-8dbe-4ede47775174
import sys
print("Hello world!!", file=sys.stderr)
Hello world!!
unaligned_seqs = qiime.Artifact.import_data(FeatureData[Sequence], 'dna-sequences.fasta')
# standard error goes to terminal where "jupyter notebook" is running
aln = alignment.methods.mafft(unaligned_seqs)
print(aln.alignment.uuid)
Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist. Command: mafft --preservecase /var/folders/xq/0kh93ng53bs6zzk091w_bbsr0000gn/T/qiime2-archive-rv181wqs/fddba98e-110d-41c1-b9c1-2748e384dfd9/data/dna-sequences.fasta 84dacdc5-0104-4c7f-a2d5-4e0c847e5bf5
sys.stderr.write('Hello world!')
Hello world!
!echo "testing" > /dev/stderr
testing
# for the sake of completeness
!cat aligned-dna-sequences.fasta
>0 ACGATCGAT-- >1 -CAGCTAGCAT
# for the sake of completeness
!cat dna-sequences.fasta
>0 ACGATCGAT >1 CAGCTAGCAT