def get_soft_text():
# OUTPUT_FILE = WORKDIR() / _fkey() ("get_soft_text.tar.gz")
# dfc = meta_df_rnaseq()
BUFFER_ALL = BUFFER_RNASEQ() + BUFFER_CHIPSEQ()
FORCE = 1
OUTDIR = WORKDIR()/_fkey()
shell.real__dir(dirname= OUTDIR)
if not FORCE and shell.file__notEmpty(OUTDIR + '.tar.gz'):
pass
else:
df_figureRegistry().to_csv(OUTDIR / 'figureRegistry.csv',index=0)
def _worker(sample):
sample = attrdict.AttrDict(sample)
sample.title = "_".join([sample[k] for k in "data_acc,age,tissue,genotype,ztime,temperature".split(",")])
res = res= pyext.jf2( template_common())
res = '\n'.join([x.strip() for x in res.splitlines()])
sample.soft_text = res
pyext.printlines([sample.soft_text], OUTDIR / pyext.f("{sample.data_acc}.soft.txt"))
# %sample.data_acc)
[_worker(sample) for sample in pyext.df__iterdict( meta_df_rnaseq().fillna("NA"))]
[_worker(sample) for sample in pyext.df__iterdict( meta_df_chipseq().fillna("NA"))]
with pyext.TempDirScope(getTempDirName=lambda: OUTDIR/'_temp',
force=1) as tdir:
tdir = tdir.d
# tdir = OUTDIR / '_temp'
shell.real__dir(dirname= tdir)
# shell.shellexec(' '.join(["tar" ,"-C",tdir,"-xvzf", INPUTDIR()/"./src/polyq-0830.get_soft_text_jaehoon.tar.gz",]))
# shell.shellexec(' '.join(["tar" ,"-C",tdir,"-xvzf", INPUTDIR()/"./src/polyq-0905.get_soft_text_Jaehoon0906.tar.gz",]))
# shell.shellexec(' '.join(["tar" ,"-C",tdir,"-xvzf", INPUTDIR()/"./src/polyq-0907.katja.get_soft_text.tar.gz",]))
shell.shellexec(' '.join(["unzip","-d",tdir, "-o",INPUTDIR()/"./src/polyq-0907-jaehoon.get_soft_text.zip", ]))
for fname in tdir.glob('*.soft.txt'):
DATA_ACC = fname.basename().replace('.soft.txt','',1)
# in df_figureRegistry()['DATA_ACC'].tolist()
assert DATA_ACC in df_figureRegistry()['DATA_ACC'].tolist(),(DATA_ACC, "JH0905")
print('[JH0906]',fname.basename(),)
pyext.file__link(fname, OUTDIR/fname.basename(),force=1)
CMD = [
"cd",OUTDIR,
"&&tar","-cvzf",OUTDIR.realpath()+'.tar.gz',"*",
]
CMD = ' '.join(pyext.stringList__flatten(CMD))
res = shell.shellexec(CMD)
def main():
temp = template_common()
samples = meta_df_rnaseq()
df = samples.fillna('NA')
samples = pyext.df__iterdict( df)
samples = list(samples)
samples = [AttrDict(x) for x in samples]
# Samples
from pprint import pprint
# pprint(samples)
# print(samples[0])
for sample in samples:
sample['rawfile_detail'] = sample_get_rawfile_detail(sample)
sample['processing_protocol'] = sample_rnaseq_processing_protocol(sample)
# processing_rnaseq_brachy(),
# for sample in samples:
pprint(sample)
# pprint(samples)
res = Template(temp, undefined=StrictUndefined).render(**locals())
res = Template(res, undefined=StrictUndefined).render(**locals())
# res = Template(res, undefined=StrictUndefined).render(**locals())
# res = pyext.jf2(temp)
# break
# res = pyext.jf2(res)
res = clean(res)
fn = (WORKDIR()+'.soft_files').makedirs_p()/sample['data_acc']+'.soft.txt'
with io.open( fn,'w',encoding='utf8') as f:
f.write(res)
# print(res)
# break
# print(template_common())
pass
def sample_init_full():
its = [
pyext.df__iterdict( meta_df_chipseq().fillna("NA")),
pyext.df__iterdict( meta_df_rnaseq().fillna("NA")),
]
it = sum(map(list,its),[])
# # it = pyext.df__iterdict( meta_df_rnaseq().fillna("NA"))
# it =( list(pyext.df__iterdict( meta_df_chipseq().fillna("NA")))
# + list(pyext.df__iterdict( meta_df_rnaseq().fillna("NA")) ))
def _worker(sample):
sample = attrdict.AttrDict(sample)
sample.title = "_".join([sample[k] for k in "data_acc,age,tissue,genotype,ztime,temperature".split(",")])
return sample
return map(_worker, it)