Stats
Description
Stats produces several output files that are useful for quality control. Examples of files produced are:
- summary statistics
- ligation heatmap plots
All figures are created as both .png and .svg files.
Command help
$ longbow stats --help
Usage: longbow stats [OPTIONS] INPUT_BAM
Calculate and produce stats on the given input bam file.
Options:
-v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG
-o, --output-prefix TEXT prefix to give to output files
-p, --pbi PATH BAM .pbi index file
-m, --model TEXT The model to use for annotation. If the given
value is a pre-configured model name, then that
model will be used. Otherwise, the given value
will be treated as a file name and Longbow will
attempt to read in the file and create a
LibraryModel from it. Longbow will assume the
contents are the configuration of a LibraryModel
as per LibraryModel.to_json(). [default: mas15]
-s, --do-simple-splitting DEPRECATED. Do splitting of reads based on
splitter delimiters, rather than whole array
structure. This splitting will cause delimiter
sequences to be repeated in each read they bound.
This is now the default setting, and this flag
has been DEPRECATED.
--help Show this message and exit.
Example
$ longbow stats input.bam
[INFO 2021-08-25 15:01:37 stats] Invoked via: longbow stats input.bam
[INFO 2021-08-25 15:01:37 stats] Using The standard MAS-seq 15 array element model.
Progress: 0 read [00:00, ? read/s]
[INFO 2021-08-25 15:01:40 stats] Processing statistics...
[INFO 2021-08-25 15:01:40 stats] Writing summary stats file...
[INFO 2021-08-25 15:01:40 stats] Writing complete ligation matrix...
[INFO 2021-08-25 15:01:50 stats] Writing reduced ligation matrix...
[INFO 2021-08-25 15:01:53 stats] Done. Elapsed time: 16.36s.
$ ls longbow_stats*
longbow_stats_00_MAS-seq_Array_Length_Counts_mas15.png
longbow_stats_00_MAS-seq_Array_Length_Counts_mas15.svg
longbow_stats_01_MAS-seq_Ligations_mas15_no_numbers.png
longbow_stats_01_MAS-seq_Ligations_mas15_no_numbers.svg
longbow_stats_02_MAS-seq_Ligations_mas15.png
longbow_stats_02_MAS-seq_Ligations_mas15.svg
longbow_stats_03_MAS-seq_Ligations_mas15_reduced_no_numbers.png
longbow_stats_03_MAS-seq_Ligations_mas15_reduced_no_numbers.svg
longbow_stats_04_MAS-seq_Ligations_mas15_reduced.png
longbow_stats_04_MAS-seq_Ligations_mas15_reduced.svg
longbow_stats_summary_stats.txt
$ cat longbow_stats_summary_stats.txt
#================================================================================
#Time: 2021-09-10 15:59:37.763512 PDT (1631314777.7635121)
#Input file: input.bam
#================================================================================
#--------------------------------------------------------------------------------
MAS-seq / Longbow Model: mas15
Total Num Reads (Arrays): 109
Total Num Array Elements (Segmented Arrays): 1635
Output yield gain: 15.00x
Num unique ligation profiles: 2
#--------------------------------------------------------------------------------
Array Length Stats:
min: 15
max: 15
mean: 15.0
median: 15.0
std: 0.0
#--------------------------------------------------------------------------------
Array Length Hist:
Length Count
0: 0
1: 0
2: 0
3: 0
4: 0
5: 0
6: 0
7: 0
8: 0
9: 0
10: 0
11: 0
12: 0
13: 0
14: 0
15: 109
#--------------------------------------------------------------------------------
Ligation Matrix Statistics:
Subdiagonal Count Total (correct segments): 1635
Off-Subdiagonal Count Total (segmentation / ligation errors): 0
Sub-Subdiagonal Count Total (missed MAS-seq adapters): 0
Correctly placed segments percentage: 100.00%
#--------------------------------------------------------------------------------
Raw Ligation Matrix:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 0
#--------------------------------------------------------------------------------
Reduced Ligation Matrix:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
109 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 109 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 109 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 109 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 109 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 109 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 109 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 109 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 109 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 109 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 109 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 109 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 109 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 109 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 109 0
#--------------------------------------------------------------------------------
Top 2 Ligation Profiles:
Profile Count Percent of All Ligations
A B C D E F G H I J K L M N O P 62 56.88%
A' B' C' D' E' F' G' H' I' J' K' L' M' N' O' P' 47 43.12%