4.1.2 Single locus
tresor.locus.simu_ampl_rate is a Python function in charge of simulating reads with respect to a series of amplication rates in the context of a given genomic locus.
Usage¶
We take the following command as an example to generate FastQ files at amplication efficiencies from 0.1 to 1.
import tresor as ts
for perm_i in range(1):
print(perm_i)
ts.locus.simu_ampl_rate(
# initial sequence generation
len_params={
'umi': {
'umi_unit_pattern': 1,
'umi_unit_len': 10,
},
'seq': 100,
},
material_params={
'fasta_cdna_fpn': to('data/Homo_sapiens.GRCh38.cdna.all.fa.gz'), # None False
},
seq_num=50,
working_dir=to('data/simu/docs/') + 'permute_' + str(perm_i) + '/',
condis=['umi', 'seq'],
sim_thres=3,
permutation=perm_i,
# PCR amplification setting
ampl_rates=np.linspace(0.1, 1, 10),
err_route='err2d', # bftree sptree err1d err2d mutation_table_minimum mutation_table_complete
pcr_error=1e-5,
pcr_num=8,
err_num_met='nbinomial', # nbinomial
# sequencing setting
seq_error=0.001,
# seq_sub_spl_number=200, # None
seq_sub_spl_rate=1, # 0.333
use_seed=True,
seed=1,
verbose=True, # True False
mode='short_read', # long_read short_read
sv_fastq_fp=to('data/simu/docs/') + 'permute_' + str(perm_i) + '/',
)
1 2 3 4 5 6 7 8 9 | |
Attributes¶
Illustration
| Attribute | Description |
|---|---|
seq_num |
number of RNA molecules. 50 by default |
len_params |
lengths of different components of a read |
seq_params |
sequences of different components of a read, It allows users to add their customised sequences |
material_params |
a Python dictionary. Showing if cDNA libraries are provided, please use key word fasta_cdna_fpn. The human cDNA library can be downloaded through the Ensembl genome database |
ampl_rates |
list of float numbers ranging from 0 to 1 |
err_route |
the computational algorithm to generate errors. There are 6 methods, including bftree, sptree, err1d, err2d, mutation_table_minimum, and mutation_table_complete. |
pcr_error |
PCR error rate |
pcr_num |
number of PCR cycles to amplify reads |
err_num_met |
the method to generate errors, that is, binomial or nbinomial |
seq_error |
sequencing error rate |
seq_sub_spl_number |
number of subsampling PCR amplified reads. It exists when seq_sub_spl_rate is specified to None |
seq_sub_spl_rate |
rate of subsampling PCR amplified reads. It exists when seq_sub_spl_number is specified to None |
sv_fastq_fp |
folder to save FastQ files |
is_seed |
if seeds are used to simulate sequencing libraries. This is designed to make in silico experiments reproducible |
working_dir |
working directory where all simulation results are about to be saved |
condis |
names of components that a read contains. It can contains an unlimited number of read components |
sim_thres |
similarity threshold. 3 by default |
permutation |
permutation times |
mode |
long_read or short_read |
verbose |
whether to print intermediate results |
| Attribute | Description |
|---|---|
cfpn |
location to the yaml configuration file. Users can specify the atrributes illustrated on the Python tab in the .yml file. |
snum |
number of sequencing molecules |
permut |
permutation times |
sthres |
similarity threshold. 3 by default |
wd |
working directory where all simulation results are about to be saved |
md |
long_read or short_read mode |
is |
if seeds are used to simulate sequencing libraries. This is designed for reproducible in silico experiments |
vb |
whether to print intermediate results |
Output¶
Console¶
17/07/2024 22:10:20 logger: Initialisation and parameters:
{'seq_params': {'custom': 'AAGC', 'custom_1': 'V'}, 'material_params': {'fasta_cdna_fpn': None}, 'mode': 'short_read', 'bead_mutation': True, 'bead_mut_rate': 0.0001, 'bead_deletion': True, 'bead_del_rate': 0.016, 'bead_insertion': True, 'bead_ins_rate': 0.1}
17/07/2024 22:10:20 logger: ======>Sequencing library preparation starts
17/07/2024 22:10:20 logger: ======>Condition map: {'umi': ['alone'], 'custom': ['alone', '1'], 'seq': ['alone']}
17/07/2024 22:10:20 logger: ======>Read 1 generation
17/07/2024 22:10:20 logger: =========>UMI generation start
17/07/2024 22:10:20 logger: ============>UMI condition 0: umi
17/07/2024 22:10:20 logger: =========>Sequence generation start
17/07/2024 22:10:20 logger: ============>Sequence condition 0: seq
17/07/2024 22:10:20 logger: ============>Custom-designed condition 0: custom
17/07/2024 22:10:20 logger: ============>Custom-designed condition 1: custom_1
17/07/2024 22:10:20 logger: ======>Read 2 generation
17/07/2024 22:10:20 logger: =========>UMI generation start
17/07/2024 22:10:20 logger: ============>UMI condition 0: umi
17/07/2024 22:10:20 logger: =========>Sequence generation start
17/07/2024 22:10:20 logger: ============>Sequence condition 0: seq
17/07/2024 22:10:20 logger: ============>Custom-designed condition 0: custom
17/07/2024 22:10:20 logger: ============>Custom-designed condition 1: custom_1
17/07/2024 22:10:20 logger: ======>Read 3 generation
17/07/2024 22:10:20 logger: =========>UMI generation start
17/07/2024 22:10:20 logger: ============>UMI condition 0: umi
17/07/2024 22:10:20 logger: =========>Sequence generation start
17/07/2024 22:10:20 logger: ============>Sequence condition 0: seq
17/07/2024 22:10:20 logger: ============>Custom-designed condition 0: custom
17/07/2024 22:10:20 logger: ============>Custom-designed condition 1: custom_1
...
19/07/2024 16:51:28 logger: ===>Sequencing library generation starts
19/07/2024 16:51:28 logger: Initialisation and parameters:
{'mode': 'short_read', 'material_params': {'fasta_cdna_fpn': 'D:\\Document\\Programming\\Python\\tresor\\tresor\\data/Homo_sapiens.GRCh38.cdna.all.fa.gz'}, 'seq_params': {'custom': 'AAGC', 'custom_1': 'A'}}
19/07/2024 16:51:28 logger: ======>Sequencing library preparation starts
19/07/2024 16:51:28 logger: ======>Condition map: {'umi': ['alone'], 'seq': ['alone']}
19/07/2024 16:51:28 logger: ======>Read CDNAs from a reference ome
19/07/2024 16:51:34 logger: ======>There are 204083 genes in the reference genome
19/07/2024 16:51:34 logger: ======>Read 1 generation
19/07/2024 16:51:34 logger: =========>UMI generation start
19/07/2024 16:51:34 logger: ============>UMI condition 0: umi
19/07/2024 16:51:34 logger: =========>Sequence generation start
19/07/2024 16:51:34 logger: ============>Sequence condition 0: seq
19/07/2024 16:51:34 logger: ======>Read 2 generation
19/07/2024 16:51:34 logger: =========>UMI generation start
19/07/2024 16:51:34 logger: ============>UMI condition 0: umi
19/07/2024 16:51:34 logger: =========>Sequence generation start
19/07/2024 16:51:34 logger: ============>Sequence condition 0: seq
...
19/07/2024 16:51:34 logger: ======>Read 49 generation
19/07/2024 16:51:34 logger: =========>UMI generation start
19/07/2024 16:51:34 logger: ============>UMI condition 0: umi
19/07/2024 16:51:34 logger: =========>Sequence generation start
19/07/2024 16:51:34 logger: ============>Sequence condition 0: seq
19/07/2024 16:51:34 logger: ======>Read 50 generation
19/07/2024 16:51:34 logger: =========>UMI generation start
19/07/2024 16:51:34 logger: ============>UMI condition 0: umi
19/07/2024 16:51:34 logger: =========>Sequence generation start
19/07/2024 16:51:34 logger: ============>Sequence condition 0: seq
19/07/2024 16:51:34 logger: ===>Time for sequencing library preparation: 6.698s
19/07/2024 16:51:35 logger: ===>Sequencing library has been generated
19/07/2024 16:51:35 logger: ===>PCR amplification starts...
19/07/2024 16:51:35 logger: ======>Assign parameters...
19/07/2024 16:51:35 logger: ======>0. Amplification rate: 0.1
19/07/2024 16:51:35 logger: ===>at PCR 1
19/07/2024 16:51:35 logger: ===>Error assignment method: err2d
19/07/2024 16:51:35 logger: ======>sampling...
19/07/2024 16:51:35 logger: ======>numbering...
19/07/2024 16:51:35 logger: ======>ordering...
19/07/2024 16:51:35 logger: =========>The number of objects to be shuffling: 50
19/07/2024 16:51:35 logger: =========>start shuffling...
19/07/2024 16:51:35 logger: =========>shuffling time: 0.0
19/07/2024 16:51:35 logger: ======>Generate PCR errors...
19/07/2024 16:51:35 logger: =========>The error 2D method is being used
19/07/2024 16:51:35 logger: ======>time for merging sequences 0.00s
19/07/2024 16:51:35 logger: ======>Summary report:
19/07/2024 16:51:35 logger: =========>PCR time: 0.00s
19/07/2024 16:51:35 logger: =========>the dimensions of the data: number of reads: (54, 3)
19/07/2024 16:51:35 logger: =========>the number of reads at this PCR: [],
19/07/2024 16:51:35 logger: =========>the number of nucleotides at this PCR: [],
19/07/2024 16:51:35 logger: =========>the number of errors at this PCR: [],
...
19/07/2024 16:51:38 logger: ===>at PCR 8
19/07/2024 16:51:38 logger: ===>Error assignment method: err2d
19/07/2024 16:51:38 logger: ======>sampling...
19/07/2024 16:51:38 logger: ======>numbering...
19/07/2024 16:51:38 logger: ======>ordering...
19/07/2024 16:51:38 logger: =========>The number of objects to be shuffling: 6400
19/07/2024 16:51:38 logger: =========>start shuffling...
19/07/2024 16:51:38 logger: =========>shuffling time: 0.004994630813598633
19/07/2024 16:51:38 logger: ======>Generate PCR errors...
19/07/2024 16:51:38 logger: =========>The error 2D method is being used
19/07/2024 16:51:39 logger: ======>time for merging sequences 0.30s
19/07/2024 16:51:39 logger: ======>Summary report:
19/07/2024 16:51:39 logger: =========>PCR time: 0.55s
19/07/2024 16:51:39 logger: =========>the dimensions of the data: number of reads: (12800, 3)
19/07/2024 16:51:39 logger: =========>the number of reads at this PCR: [],
19/07/2024 16:51:39 logger: =========>the number of nucleotides at this PCR: [],
19/07/2024 16:51:39 logger: =========>the number of errors at this PCR: [],
19/07/2024 16:51:39 logger: ======>PCR amplification completes in 1.1190292835235596s
19/07/2024 16:51:39 logger: ======>Sequencing starts
19/07/2024 16:51:39 logger: ======>sampling...
19/07/2024 16:51:39 logger: ======>Generate sequencing errors...
19/07/2024 16:51:39 logger: =========>There are 12800 reads to be sequenced
19/07/2024 16:51:39 logger: =========>The position table construction starts
19/07/2024 16:51:39 logger: =========>Time for constructing the position table: 0.196s
19/07/2024 16:51:39 logger: =========>There are 1408000 nucleotides to be sequenced
19/07/2024 16:51:39 logger: =========>Determination of number of sequencing errors start
19/07/2024 16:51:39 logger: ============>There are 1388 nucleotide errors during sequencing
19/07/2024 16:51:39 logger: =========>Time for determining sequencing errors: 0.000s
19/07/2024 16:51:39 logger: =========>Sequencing error Assignment starts
19/07/2024 16:51:39 logger: =========>Time for assigning sequencing errors: 0.10s
19/07/2024 16:51:39 logger: =========>Sequencing time: 0.37s
19/07/2024 16:51:39 logger: =========>Sequencing has completed
19/07/2024 16:51:39 logger: =========>Reads write to files in FastQ format
======>simulation completes in 4.705037355422974s
19/07/2024 16:51:39 logger: =========>FastQ file is saved
19/07/2024 16:51:39 logger: ======>Simulation completes
===>Time: 11.667s
Finished!
Understanding files¶
The resultant files of the simulated reads are shown as follows.
