def outdir_two_files_gap(tmpdir_factory, fpath_fasta) -> str:
# Output directory with following files:
# `file_combinator_adjacent_contigs.tsv`
# `file.2_combinator_adjacent_contigs.tsv`
outdpath: str = tmpdir_factory.mktemp('outdir-three-files')
fls.make_outdir(outdpath)
# Configure path to origin output file
origin_fpath: str = os.path.join(
outdpath, '{}_combinator_adjacent_contigs.tsv'.format(
fls.conf_prefix(fpath_fasta, outdpath)))
# Create origin output file
with open(origin_fpath, 'w') as tmpfile:
pass
# end with
# Create numbered (numbers 1, 2) files
i: int
for i in range(2):
with open(
os.path.join(
outdpath, '{}_combinator_adjacent_contigs.tsv'.format(
fls.conf_prefix(fpath_fasta, outdpath))),
'w') as tmpfile:
pass
# end with
# end for
# And remove file number 1
os.unlink(os.path.join(outdpath, 'file.1_combinator_adjacent_contigs.tsv'))
return outdpath
def outdir_single_numbered(tmpdir_factory, fpath_fasta) -> str:
# Output directory with following files:
# `file.1_combinator_adjacent_contigs.tsv`
outdpath: str = tmpdir_factory.mktemp('outdir-two-files')
fls.make_outdir(outdpath)
# Configure path to origin output file
origin_fpath: str = os.path.join(
outdpath, '{}_combinator_adjacent_contigs.tsv'.format(
fls.conf_prefix(fpath_fasta, outdpath)))
# Create origin output file
with open(origin_fpath, 'w') as tmpfile:
pass
# end with
# Create numbered (number 1) file
with open(
os.path.join(
outdpath, '{}_combinator_adjacent_contigs.tsv'.format(
fls.conf_prefix(fpath_fasta, outdpath))), 'w') as tmpfile:
pass
# end with
# And remove origin file
os.unlink(origin_fpath)
return outdpath
def outdir_single_file(tmpdir_factory, fpath_fasta) -> str:
# Output directory with single `file__combinator_adjacent_contigs.tsv` file
outdpath: str = tmpdir_factory.mktemp('outdir-single-file')
fls.make_outdir(outdpath)
# Configure path to origin output file
origin_fpath: str = os.path.join(
outdpath, '{}_combinator_adjacent_contigs.tsv'.format(
fls.conf_prefix(fpath_fasta, outdpath)))
# Create origin output file
with open(origin_fpath, 'w') as tmpfile:
pass
# end with
return outdpath
def test_make_outdir(self, tmpdir: str):
# Should successfully make a directory in `tempdir`
# and create a file in it.
outdpath: str = os.path.join(tmpdir, 'outdir')
fls.make_outdir(outdpath)
assert os.path.isdir(outdpath)
tesf_fpath = os.path.join(outdpath, 'test.file.txt')
with open(tesf_fpath, 'w') as testfile:
pass
# end with
assert os.path.isfile(tesf_fpath)
def main(version: str, last_update_date: str) -> None:
contigs_fpaths: Sequence[str] # paths to input files
params: Dict[str, Any] # parameters of the program
# Parse command line arguments
contigs_fpaths, params = parse_args(version, last_update_date)
# Report parameters of current run
_report_parameters(params, version, last_update_date)
# Iterate over input files and process them
fpath: str
for fpath in contigs_fpaths:
print('Processing file `{}`'.format(fpath))
# Create output dir
make_outdir(params['o'])
# Read contigs
contig_collection: cnt.ContigCollection = cnt.get_contig_collection(
fpath, params['a'])
# Detect adjacent contigs
overlap_collection: ovl.OverlapCollection = ovl.detect_adjacent_contigs(
contig_collection, params['i'], params['a'])
# Assign multiplicity to contigs
amu.assign_multiplty(contig_collection, overlap_collection)
# Make prefix for current input file
prefix: str = conf_prefix(fpath, params['o'])
# Write output files
# Write adjacency table
out.write_adjacency_table(contig_collection, overlap_collection,
params['o'], prefix)
# Write full log
out.write_full_log(contig_collection, overlap_collection, params['o'],
prefix)
# Write summary
out.write_summary(contig_collection, overlap_collection, fpath,
params['o'], prefix)
print('-' * 20)
def empty_outdir(tmpdir_factory) -> str:
# Empty output directory
outdpath: str = tmpdir_factory.mktemp('empty-outdir')
fls.make_outdir(outdpath)
return outdpath