Commit 55f1e0ba authored by yy1533's avatar yy1533
Browse files

🐾

parent 040d2014
......@@ -41,7 +41,7 @@ def bc_dict_seq2id(bc_index_fpath, col_seq=None):
if row.startswith('#'):
continue
row = row.strip().split()
print('{}:{}'.format(row_num, row))
# print('{}:{}'.format(row_num, row))
row_val = row[col_seq]
row_key = row_num
out[row_key] = row_val
......@@ -63,7 +63,7 @@ def bc_dict_id2seq(bc_index_fpath, col_seq=None):
if row.startswith('#'):
continue
row = row.strip().split()
print('{}:{}'.format(row_num, row))
# print('{}:{}'.format(row_num, row))
row_val = row[col_seq]
row_key = row_num
out[row_key] = row_val
......
__version__ = '0.4.3'
__version__ = '0.4.4'
......@@ -122,6 +122,14 @@ rule Count_Matrix:
touch('_done_UMI')
message: 'Finished counting UMI-count matrix.'
run:
if ALIGNER == 'star':
shell('rm {}'.format('_done_star_genome_loaded'))
print('Free memory loaded by STAR', flush=True)
cmd = 'STAR '
cmd += '--genomeLoad Remove '
cmd += '--genomeDir {STAR_INDEX_DIR} '
shell(cmd)
print_logger('UMI-count matrix is saved at {}'.format(input.csv))
......@@ -162,17 +170,17 @@ rule celseq2:
run:
if glob.glob('celseq2_job*.sh*'):
shell('mv -f celseq2_job*.sh* {}'.format(SUBDIR_QSUB))
print_logger('Expression UMI matrix is saved at {}'.format(input.csv))
if ALIGNER == 'star':
shell('rm {}'.format(rules.star_load_genome.output))
shell('rm {}'.format('_done_star_genome_loaded'))
print('Free memory loaded by STAR', flush=True)
cmd = 'STAR '
cmd += '--genomeLoad Remove '
cmd += '--genomeDir {STAR_INDEX_DIR} '
shell(cmd)
print_logger('Expression UMI matrix is saved at {}'.format(input.csv))
rule setup_dir:
input: SAMPLE_TABLE_FPATH
output:
......
......@@ -10,14 +10,14 @@
---
## :fa-flag-checkered: **v0.4.3**
## :fa-flag-checkered: **v0.4.4**
:fa-calendar: **2018-02-13**
:fa-star: **Features**
- Improve the design of snakemake pipeline to avoid silent pre-inhibition.
- Better support STAR to avoid memory overuse.
- Improve the design of `snakemake` pipeline to avoid silent pre-inhibition.
- Improve running with STAR to avoid memory over-use.
---
......
......@@ -112,6 +112,7 @@ setup(
# 'sphinx-argparse',
# 'mock',
'mkdocs',
'mkdocs-material',
'fontawesome_markdown',
'mkdocs-bootswatch',
'pymdown-extensions',
......
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