def get_targets(units,
assembly_basename,
outdir,
extensions=['/quant.sf', '/lib_format_counts.json'],
se_ext=['se'],
pe_ext=['pe']):
"""
Use the sample info provided in the tsv file
to generate required targets for salmon
"""
salmon_targs = []
# here we need to get all units belonging to a single sample.
# When I used 'groupby' on our initial test data, groups were
# A/AB, B/AB, rather than A, B, AB. I'm sure there's a way to
# do exact matching in groupby, but here's a hackaround for now.
samples = list(set(units['sample'].tolist()))
#by_sample = units.groupby(['sample'], sort = False)
for s in samples:
unit_list = units.groupby(level=0).get_group(s)['unit'].tolist()
for unit in unit_list:
if is_se(units, s, unit):
salmon_targs = salmon_targs + [
'{}_{}_x_{}'.format(s, se_ext[0], assembly_basename) + i
for i in extensions
]
else:
salmon_targs = salmon_targs + [
'{}_{}_x_{}'.format(s, pe_ext[0], assembly_basename) + i
for i in extensions
]
salmon_targs = list(set(salmon_targs)) # elim any redundant targs
return [path.join(outdir, targ) for targ in salmon_targs]
def get_khmer_trimmed_trinity_input(units, basename, outdir, extensions = ['.gz'], se_ext = ['.se'], pe_ext = ['.paired.1','.paired.2', '.single']):
"""
Use the sample info provided in the tsv file
to generate required targets for trimmomatic
"""
targs = []
for s, u in units.iterrows():
sample, unit = u['sample'],u['unit']
end = se_ext if is_se(units,sample, unit) else pe_ext
targs = targs + ['{}_{}_'.format(sample, unit) + i + j for i in end for j in extensions]
return [join(outdir, targ) for targ in targs]
def get_targets(units,
basename,
outdir,
extensions=['.fq.gz'],
se_ext=['se'],
pe_ext=['1', '2']):
"""
Use the sample info provided in the tsv file
to generate required targets for cat_reads_by_unit
"""
cat_targs = []
for s, u in units.iterrows():
sample, unit = u['sample'], u['unit']
end = se_ext if is_se(units, sample, unit) else pe_ext
cat_targs = cat_targs + [
'{}_'.format(sample) + i + j for i in end for j in extensions
]
return [path.join(outdir, targ) for targ in cat_targs]
def get_targets(units,
basename,
outdir,
extensions=['.trim.fq.gz'],
se_ext=['se'],
pe_ext=['1', '2']):
"""
Use the sample info provided in the tsv file
to generate required targets for trimmomatic
"""
trim_targs = []
for s, u in units.iterrows():
sample, unit = u['sample'], u['unit']
end = se_ext if is_se(units, sample, unit) else pe_ext
trim_targs = trim_targs + [
'{}_{}_'.format(sample, unit) + i + j for i in end
for j in extensions
]
#trim_targs = trim_targs + ['{}_'.format(sample) + i + j for i in end for j in extensions]
#trim_targs = list(set(trim_targs))
return [path.join(outdir, targ) for targ in trim_targs]