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[DOC] Fix docs about biom format #195

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[DOC] Fix docs about biom format #195

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20 changes: 10 additions & 10 deletions scripts/deblur
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Original file line number Diff line number Diff line change
Expand Up @@ -353,10 +353,10 @@ def remove_chimeras_denovo(seqs_fp, output_fp, log_level, log_file):

# GENERATE BIOM TABLE COMMAND
@deblur_cmds.command()
@click.argument('seqs_fp', required=True,
@click.argument('seqs_dir', required=True,
type=click.Path(resolve_path=True, readable=True, exists=True,
file_okay=True))
@click.argument('output_biom_fp', required=True,
@click.argument('output_biom_dir', required=True,
type=click.Path(resolve_path=True, readable=True,
exists=False, file_okay=True))
@click.option('--min-reads', required=False, type=int, default=10,
Expand All @@ -376,28 +376,28 @@ def remove_chimeras_denovo(seqs_fp, output_fp, log_level, log_file):
exists=False, dir_okay=True),
default='deblur.log',
show_default=True, help="log file name")
def build_biom_table(seqs_fp, output_biom_fp, min_reads, file_type, log_level,
def build_biom_table(seqs_dir, output_biom_dir, min_reads, file_type, log_level,
log_file):
"""Generate a BIOM table from a directory of chimera removed fasta files
Parameters
----------
seqs_fp : str
seqs_dir : str
the path to the directory containing the chimera removed fasta files
output_biom_fp : str
the path where to save the output biom table files
('all.biom', 'reference-hit.biom', 'reference-non-hit.biom')
output_biom_dir : str
the directory where to save the output biom table files
('all.biom', 'all.seq.fa')
file_type : str
the files type to add to the table
(default='.trim.derep.no_artifacts.msa.deblur.no_chimeras',
can be '.fasta' or '.fa' if needed)
"""
start_log(level=log_level * 10, filename=log_file)
output_filename = 'all.biom'
output_fp = join(output_biom_fp, output_filename)
output_fp = join(output_biom_dir, output_filename)
outputfasta_filename = 'all.seq.fa'
outputfasta_fp = join(output_biom_fp, outputfasta_filename)
outputfasta_fp = join(output_biom_dir, outputfasta_filename)

samples = get_files_for_table(seqs_fp, file_type)
samples = get_files_for_table(seqs_dir, file_type)
create_otu_table(output_fp, samples,
outputfasta_fp=outputfasta_fp, minreads=min_reads)

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