3.2 Bulk RNA seq
ts.spsimseq_bulk is the module that can simulate reads consisting of only UMIs per each, or UMI+Genomic sequence per each. The general-purpose design gives the module this name. To achieve this purpose, a case-study CLI should look like below:
Usage¶
import tresor as ts
gspl = ts.gmat.spsimseq_bulk(
R_root='D:/Programming/R/R-4.3.2/',
num_samples=2,
num_genes=10,
simulator='spsimseq',
sv_fpn=to('data/spsimseq_bulk.h5'),
)
print(gspl)
tresor gmat_bulk \
-rfpn D:/Programming/R/R-4.3.2/ \
-nspl 2 \
-ngene 10 \
-gsimulator spsimseq \
-wd ./tresor/data/spsimseq_bulk.h5 \
-is True \
-vb True
Attributes¶
Illustration
bubble_sort.py
R_root='D:/Programming/R/R-4.3.2/',
num_samples=2,
num_genes=10,
simulator='spsimseq',
sv_fpn=to('data/spsimseq_bulk.h5'),
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3. Nulla tempor lobortis orci
Output¶
12/12/2023 02:02:41 logger: =========>spsimseq is being used
SPsimSeq package version 1.12.0
R[write to console]: Estimating featurewise correlations ...
R[write to console]: Selecting candidate DE genes ...
R[write to console]: Estimating densities ...
R[write to console]: Configuring design ...
R[write to console]: Simulating data ...
R[write to console]: ...1 of 1
12/12/2023 02:02:48 logger: =========>spsimseq completes simulation
Gene_1 Gene_2 Gene_3 Gene_4 ... Gene_7 Gene_8 Gene_9 Gene_10
Sample_1 0.0 0.0 0.0 0.0 ... 322.0 425.0 7.0 1202.0
Sample_2 1.0 2.0 2.0 2.0 ... 633.0 423.0 87.0 1619.0
[2 rows x 10 columns]