bedtools/bedtools_groupby

groupby

BED

Description

Summarizes a dataset column based upon common column groupings.
Akin to the SQL "group by" command.

Inputs

Name	Type & Properties	Description
--input -i	file required	The input BED file to be used.

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	The output groupby BED file.

Name

Type & Properties

--output

file

required

output

Options

Name	Type & Properties	Description
--groupby -g -grp	string required	Specify the columns (1-based) for the grouping. The columns must be comma separated. - Default: 1,2,3
--column -c -opCols	integer required	Specify the column (1-based) that should be summarized.
--operation -o -ops	string	Specify the operation that should be applied to opCol. Valid operations: sum, count, count_distinct, min, max, mean, median, mode, antimode, stdev, sstdev (sample standard dev.), collapse (i.e., print a comma separated list (duplicates allowed)), distinct (i.e., print a comma separated list (NO duplicates allowed)), distinct_sort_num (as distinct, but sorted numerically, ascending), distinct_sort_num_desc (as distinct, but sorted numerically, descending), concat (i.e., merge values into a single, non-delimited string), freqdesc (i.e., print desc. list of values:freq) freqasc (i.e., print asc. list of values:freq) first (i.e., print first value) last (i.e., print last value) Default value: sum If there is only column, but multiple operations, all operations will be applied on that column. Likewise, if there is only one operation, but multiple columns, that operation will be applied to all columns. Otherwise, the number of columns must match the the number of operations, and will be applied in respective order. E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5, the mean of column 4, and the count of column 6. The order of output columns will match the ordering given in the command.
--full	boolean_true	Print all columns from input file. The first line in the group is used. Default: print only grouped columns.
--inheader	boolean_true	Input file has a header line - the first line will be ignored.
--outheader	boolean_true	Print header line in the output, detailing the column names. If the input file has headers (-inheader), the output file will use the input's column names. If the input file has no headers, the output file will use "col_1", "col_2", etc. as the column names.
--header	boolean_true	same as '-inheader -outheader'.
--ignorecase	boolean_true	Group values regardless of upper/lower case.
--precision -prec	integer	Sets the decimal precision for output.
--delimiter -delim	string	Specify a custom delimiter for the collapse operations.

Name

Type & Properties

--groupby

-g

-grp

string

required

--column

-c

-opCols

integer

required

--operation

-o

-ops

string

--full

boolean_true

--inheader

boolean_true

--outheader

boolean_true

--header

boolean_true

--ignorecase

boolean_true

--precision

-prec

integer

--delimiter

-delim

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.bed"  
precision: [ 5 ]  
delimiter: [ "," ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/bedtools/bedtools_groupby/main.nf \  
  -params-file params.yaml

bedtools/bedtools_groupby

Inputs

Outputs

Options

Run this component

Relationships

Used by

Uses