def run(targets):
# try to run without converting to json, if that fails,
# convert first, then run on the json-converted biom file
if os.stat(file).st_size < 1:
for target in targets:
open(target, "w").close()
return True
return strategies.backup(
(strategies.Group(CmdAction(cmd1%(file), verbose=verbose),
CmdAction(cmd2%(norm_out), verbose=verbose)),
strategies.Group(format_cmd,
CmdAction(cmd1%(converted), verbose=verbose),
CmdAction(cmd2%(norm_out), verbose=verbose)))
)
def run():
return strategies.backup(
(CmdAction(cmd+opts, verbose=verbose),
strategies.Group(
PythonAction(_revcomp),
CmdAction(cmd+revcomp_opts,verbose=verbose))),
extra_conditions=[output_exists]
)
def run(targets):
strategies.backup(
(CmdAction(cmd.format(input_fname),verbose=verbose),
strategies.Group(
CmdAction(revcomp_cmd),
CmdAction(cmd.format(revcomp_fname),verbose=verbose))),
extra_conditions = [
lambda ret, output_fname: os.stat(output_fname).st_size == 0
],
output_fname=output_fname
)
def run():
r1, r2 = input_fastq_pair
paired = lambda s: s.replace('.fastq', '_paired.fastq')
ret = strategies.backup(
(CmdAction(stitch_cmd.format(
r1=r1, r2=r2, opts_str=opts_str, output_fastq=output_fastq),
verbose=verbose),
strategies.Group(
CmdAction(pair_cmd.format(
r1=r1, r2=r2, r1out=paired(r1), r2out=paired(r2)),
verbose=verbose),
CmdAction(stitch_cmd.format(r1=paired(r1),
r2=paired(r2),
opts_str=opts_str,
output_fastq=output_fastq),
verbose=verbose)),
CmdAction('cp {r1} {out}'.format(r1=r1, out=output_fastq),
verbose=verbose)), )
if remove_tempfiles:
for f in (paired(r1), paired(r2)):
if os.path.exists(f):
os.remove(f)
return ret