Console usage
All console scripts require configuration file – tab separated file with columns:
Column NAMES should NOT be INCLUDED in real configuration file.
<ins>Group name</ins> |
<ins>Path to report</ins> |
<ins>Path to annotation</ins> |
Flank length |
Min region length |
Region type |
Genome type |
Report type |
|---|---|---|---|---|---|---|---|
Mock |
mock-1.CX_report.txt |
annotation.gff |
2000 |
0 |
gene |
gff |
bismark |
Mock |
mock-2.CX_report.txt |
annotation.gff |
2000 |
0 |
gene |
gff |
bismark |
Infected |
infected-1.CX_report.txt |
annotation.gff |
2000 |
0 |
gene |
gff |
bismark |
Infected |
infected-2.CX_report.txt |
annotation.gff |
2000 |
0 |
gene |
gff |
bismark |
Columns with <ins>underlined</ins> are required.
bsxplorer-metagene
usage: bsxplorer-metagene [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
[--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS]
config
Metagene report creation tool
positional arguments:
config Path to config file
options:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_08-07-24_18-47-26)
--dir DIR Output and working dir (default: /Users/shitohana/Desktop/PycharmProjects/BSXplorer/tests)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t, --threads Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
-s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
Summary function to calculate density for bin with. (default: wmean)
-u UBIN, --ubin UBIN Number of windows for upstream region (default: 50)
-d DBIN, --dbin DBIN Number of windows for downstream downstream (default: 50)
-b BBIN, --bbin BBIN Number of windows for body region (default: 100)
-q QUANTILE, --quantile QUANTILE
Quantile of most varying genes to draw on clustermap (default: 0.75)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 10)
-H VRESOLUTION Vertical resolution for heat-map (default: 100)
-V HRESOLUTION Vertical resolution for heat-map (default: 100)
--separate_strands Do strands need to be processed separately (default: False)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--ticks TICKS TICKS TICKS TICKS TICKS
Names of ticks (- character should be escaped with double reverse slash) (default: None)
Example
Intraspecies report.
Command:
bsxplorer-metagene --dir metagene -o metagene_intra -m 30 -u 100 -b 200 -d 100 -q 0.95 -C 0.95 -S 10 -H 50 -V 50 --export pdf --ticks \\-2000bp \\ Body \\ +2000bp metagene.conf
Sample name |
Report path |
Annot path |
Flank length |
Min length |
Region type |
Annot format |
Report format |
|---|---|---|---|---|---|---|---|
AraTh |
A_thaliana.txt |
A_thaliana_genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
BraDi |
Brachypodium_distachyon_leaf.txt |
Brachypodium_distachyon_genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
CucSa |
C_sativus.txt |
C_sativus_genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
MusMu |
SRR16815382_Mus_musculus.CX_report.gz |
Mus_musculus_genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Same species report.
Command:
bsxplorer-metagene --dir metagene-brapa -o metagene_brapa -m 30 -u 100 -b 200 -d 100 -q 0.95 -C 0.95 -S 10 -H 50 -V 50 --export pdf --ticks \\-2000bp \\ Body \\ +2000bp brapa.conf
Sample name |
Report path |
Annot path |
Flank length |
Min length |
Region type |
Annot format |
Report format |
|---|---|---|---|---|---|---|---|
Misugi_mock |
DRR336466.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Misugi_mock |
DRR336467.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Misugi_infected |
DRR336468.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Misugi_infected |
DRR336469.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Nanane_mock |
DRR336470.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Nanane_mock |
DRR336471.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Nanane_infected |
DRR336472.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
Nanane_infected |
DRR336473.CX_report.txt |
genomic.gff |
2000 |
0 |
gene |
gff |
bismark |
bsxplorer-category
usage: bsxplorer-categorise [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
[--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS] [--cytosine_p CYTOSINE_P] [--min_cov MIN_COV] [--region_p REGION_P] [--save_cat | --no-save_cat]
config
BM, UM categorisation tool
positional arguments:
config Path to config file
options:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_08-07-24_18-49-15)
--dir DIR Output and working dir (default: /Users/shitohana/Desktop/PycharmProjects/BSXplorer/tests)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t, --threads Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
-s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
Summary function to calculate density for bin with. (default: wmean)
-u UBIN, --ubin UBIN Number of windows for upstream region (default: 50)
-d DBIN, --dbin DBIN Number of windows for downstream downstream (default: 50)
-b BBIN, --bbin BBIN Number of windows for body region (default: 100)
-q QUANTILE, --quantile QUANTILE
Quantile of most varying genes to draw on clustermap (default: 0.75)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 10)
-H VRESOLUTION Vertical resolution for heat-map (default: 100)
-V HRESOLUTION Vertical resolution for heat-map (default: 100)
--separate_strands Do strands need to be processed separately (default: False)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--ticks TICKS TICKS TICKS TICKS TICKS
Names of ticks (- character should be escaped with double reverse slash) (default: None)
--cytosine_p CYTOSINE_P
P-value for binomial test to consider cytosine methylated (default: .05)
--min_cov MIN_COV Minimal coverage for cytosine to keep (default: 2)
--region_p REGION_P P-value for binomial test to consider region methylated (default: .05)
--save_cat, --no-save_cat
Does categories need to be saved (default: True)
bsxplorer-chr
usage: bsxplorer-chr [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t THREADS] [-w WINDOW] [-l MIN_LENGTH] [-C CONFIDENCE] [-S SMOOTH] [--export {pdf,svg,none}] [--separate_strands] config
Chromosome methylation levels visualisation tool
positional arguments:
config Path to config file
options:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_08-07-24_18-47-14)
--dir DIR Output and working dir (default: /Users/shitohana/Desktop/PycharmProjects/BSXplorer/tests)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t THREADS, --threads THREADS
Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: True)
-w WINDOW, --window WINDOW
Length of windows in bp (default: 1000000)
-l MIN_LENGTH, --min_length MIN_LENGTH
Minimum length of chromosome to be analyzed (default: 1000000)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 100)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--separate_strands Do strands need to be processed separately (default: False)
Example
Command:
bsxplorer-metagene --dir metagene -o metagene_intra -m 30 -u 100 -b 200 -d 100 -q 0.95 -C 0.95 -S 10 -H 50 -V 50 --export pdf --ticks \\-2000bp \\ Body \\ +2000bp metagene.conf
Config file: Example config file (brapa.conf)
bsxplorer-bam
usage: bsxplorer-bam [-h] --bam BAM --bai BAI [-f FASTA] [--bamtype {bismark}] [-m {report,stats}] [--to_type {bismark,cgmap,bedgraph,coverage,binom}] [--stat {ME,EPM,PDR}] [--stat_param STAT_PARAM] [--stat_md STAT_MD]
[-g GFF] [-c {CG,CHG,CHH,all}] [-q {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42}] [-s] [--no_qc] [-t THREADS] [-n BATCH_N]
[-a READAHEAD]
output
BAM to report reader converter tool.
positional arguments:
output Path to output file.
options:
-h, --help show this help message and exit
--bam BAM Path to SORTED .bam file with alignments (default: None)
--bai BAI Path to .bai index file (default: None)
-f FASTA, --fasta FASTA
Path to .fasta file with reference sequence for full cytosine report. (default: None)
--bamtype {bismark} Type of aligner which was used for generating BAM. (default: bismark)
-m {report,stats}, --mode {report,stats}
--to_type {bismark,cgmap,bedgraph,coverage,binom}
Specifies the output file type if mode is set to 'report'. (default: bismark)
--stat {ME,EPM,PDR} Specifies the BAM stat type if mode is set to 'stats' (default: ME)
--stat_param STAT_PARAM
See docs for specifical stat parameters. (default: 4)
--stat_md STAT_MD Minimum number of reads for cytosine to be analysed (if mode is 'stats') (default: 4)
-g GFF, --gff GFF Path to regions genome coordinates .gff file, if cytosines need to be filtered. (default: None)
-c {CG,CHG,CHH,all}, --context {CG,CHG,CHH,all}
Filter cytosines by specific methylation context (default: all)
-q {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42}, --min_qual {0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42}
Filter cytosines by read Phred score quality (default: None)
-s, --skip_converted Skip reads aligned to converted sequence (default: False)
--no_qc Do not calculate QC stats (default: False)
-t THREADS, --threads THREADS
How many threads will be used for reading the BAM file. (default: 1)
-n BATCH_N, --batch_n BATCH_N
Number of reads per batch. (default: 10000.0)
-a READAHEAD, --readahead READAHEAD
Number of batches to be read before processing. (default: 5)