wilkelab / Opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
21 stars 5 forks source link

blast command contains errant float #72

Closed jimrybarski closed 4 years ago

jimrybarski commented 4 years ago

e_value just needs to get cast to a float in build_blastp_command()

['blastp', '-query', '/tmp/tmpxnq8bkg7/all_orfs.fasta', '-db', 'fixed-nonredundant-transposases.fasta', '-evalue', 0.001, '-out', '/tmp/tmp7ro79017/blast_out.tsv', '-outfmt', '6 qseqid sseqid stitle evalue         bitscore score length pident         nident mismatch positive gapopen         gaps ppos qcovhsp qseq']
Traceback (most recent call last):
  File "pipelinetest.py", line 14, in <module>
    results = p.run(filename, outfrmt="CSV", outfile=outfile, gzip=True)
  File "/mnt/marble/hdd/home/jim/CRISPR-Transposons/src/crisposon/pipeline.py", line 427, in run
    step.execute(self._all_orfs, self.span)
  File "/mnt/marble/hdd/home/jim/CRISPR-Transposons/src/crisposon/steps.py", line 200, in execute
    super().execute(orfs)
  File "/mnt/marble/hdd/home/jim/CRISPR-Transposons/src/crisposon/steps.py", line 190, in execute
    self.hits = self.search_tool.run(orfs)
  File "/mnt/marble/hdd/home/jim/CRISPR-Transposons/src/crisposon/steps.py", line 38, in run
    subprocess.run(cmd, check=True)
  File "/mnt/marble/hdd/home/jim/py36/lib/python3.6/subprocess.py", line 403, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/mnt/marble/hdd/home/jim/py36/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/mnt/marble/hdd/home/jim/py36/lib/python3.6/subprocess.py", line 1275, in _execute_child
    restore_signals, start_new_session, preexec_fn)
TypeError: expected str, bytes or os.PathLike object, not float