7. Summary¶
These tables summarize BEDOPS utilities by option, file inputs and BED column requirements.
7.1. Set operation and statistical utilities¶
7.1.1. bedextract
¶
Efficiently extracts features from BED input.
BEDOPS bedextract documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
|
Print every chromosome found in |
1 |
1 |
3 |
|
Retrieve all rows for specified chromosome, e.g. |
1 |
1 |
3 |
|
Grab elements of |
2 |
2 |
3 |
7.1.2. bedmap
¶
Maps source signals from
map-file
onto qualified target regions fromref-file
. Calculates an output for everyref-file
element.BEDOPS bedmap documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
|
Reports the total number of bases from |
1 |
2 |
3 |
|
Reports the number of distinct bases from |
1 |
2 |
3 |
|
Reports the fraction of distinct bases from |
1 |
2 |
3 |
|
Require |
1 |
2 |
3 |
|
Process data for given |
1 |
2 |
3 |
|
Reports the number of overlapping elements in |
1 |
2 |
3 |
|
Reports the Coefficient of Variation: the result of |
1 |
2 |
5 |
|
Error-check all input files (slower). |
1 |
2 |
3 |
|
Echo each line from |
1 |
2 |
3 |
|
Reports the overlapping elements found in |
1 |
2 |
3 |
|
Reports the IDs (4th column) from overlapping |
1 |
2 |
4 |
|
List unique IDs from overlapping |
1 |
2 |
4 |
|
Reports the genomic range of overlapping elements from |
1 |
2 |
3 |
|
Reports the scores (5th column) from overlapping |
1 |
2 |
5 |
|
Calculates difference between start and stop coordinates (or size) of each mapped element. |
1 |
2 |
3 |
|
Calculates size of overlap between each mapped element and its reference element. |
1 |
2 |
3 |
|
Reports the first 3 fields of |
1 |
2 |
3 |
|
Reports the length of the |
1 |
2 |
3 |
|
(Advanced) Strong input assumptions are made. Review documents
before use. Compatible with |
1 |
2 |
5 |
|
The fraction of the element’s size from |
1 |
2 |
5 |
|
The fraction of the element’s size from |
1 |
2 |
5 |
|
Both |
1 |
2 |
5 |
|
Both |
1 |
2 |
5 |
|
Shorthand for |
1 |
2 |
5 |
|
Reports the presence of one or more overlapping elements in
|
1 |
2 |
3 |
|
Reports the value at the k th fraction. A generalized median-like
calculation, where |
1 |
2 |
5 |
|
Reports the ‘median absolute deviation’ of overlapping elements in
|
1 |
2 |
5 |
|
Reports the highest score from overlapping elements in |
1 |
2 |
5 |
|
The lexicographically “smallest” element with the highest score from
overlapping elements in |
1 |
2 |
5 |
|
A randomly-chosed element with the highest score from overlapping
elements in |
1 |
2 |
5 |
|
Reports the average score from overlapping elements in |
1 |
2 |
5 |
|
Reports the median score from overlapping elements in |
1 |
2 |
5 |
|
Reports the lowest score from overlapping elements in |
1 |
2 |
5 |
|
The lexicographically “smallest” element with the lowest score from
overlapping elements in |
1 |
2 |
5 |
|
A randomly-chosed element with the lowest score from overlapping
elements in |
1 |
2 |
5 |
|
Omits printing reference elements which do not associate with any mapped elements. |
1 |
2 |
3 |
|
Reports the square root of the result of |
1 |
2 |
5 |
|
Reports the accumulated value from scores of overlapping elements in
|
1 |
2 |
5 |
|
Reads through entire |
1 |
2 |
3 |
|
Reports the mean score from overlapping elements in |
1 |
2 |
5 |
|
Reports the variance of scores from overlapping elements in
|
1 |
2 |
5 |
7.1.3. bedops
¶
Offers set and multiset operations for files in BED format.
BEDOPS bedops documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
|
Process data for given |
1 |
No imposed limit |
3 |
|
Reports the intervening intervals between the input coordinate segments. |
1 |
No imposed limit |
3 |
|
Breaks up merged regions into fixed-size chunks, optionally anchored on start coordinates a fixed distance apart. |
1 |
No imposed limit |
3 |
|
Reports the intervals found in the first file that are not present in any other input file. |
2 |
No imposed limit |
3 |
|
Error-check input files (slower). |
1 |
No imposed limit |
3 |
|
Reports rows from the first file that overlap, by a specified percentage or number of base pairs, the merged segments from all other input files. |
2 |
No imposed limit |
3 |
|
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. |
1 |
No imposed limit |
3 |
|
Reports the intervals common to all input files. |
2 |
No imposed limit |
3 |
|
Reports intervals from all input files, after merging overlapping and adjoining segments. |
1 |
No imposed limit |
3 |
|
Reports exactly everything that |
2 |
No imposed limit |
3 |
|
Reports all disjoint intervals from all input files. Overlapping segments are cut up into pieces at all segment boundaries. |
1 |
No imposed limit |
3 |
|
Add |
1 |
No imposed limit |
3 |
|
Pad input file(s) coordinates symmetrically by |
1 |
No imposed limit |
3 |
|
Reports the intervals found in exactly one input file. |
2 |
No imposed limit |
3 |
|
Reports the intervals from all input files in sorted order. Duplicates are retained in the output. |
1 |
No imposed limit |
3 |
7.1.4. closest-features
¶
For every element in
input-file
, find those elements inquery-file
nearest to its left and right edges.BEDOPS closest-features documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
2 |
2 |
3 |
|
Process data for given |
2 |
2 |
3 |
|
Output includes the signed distances between the |
2 |
2 |
3 |
|
Error-check all input files (slower). |
2 |
2 |
3 |
|
Do not consider elements that overlap. Overlapping elements, otherwise, have highest precedence. |
2 |
2 |
3 |
|
Do not echo elements from |
2 |
2 |
3 |
|
Choose the nearest element from |
2 |
2 |
3 |
7.2. Sorting¶
7.2.1. sort-bed
¶
Sorts input BED file(s) into the order required by other utilities. Loads all input data into memory.
BEDOPS sort-bed documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
1 |
1000 |
3 |
|
|
1 |
1000 |
3 |
|
Report unique elements (those which only occur once) in output. |
1 |
1000 |
3 |
|
Report duplicate elements (those which occur 2+ times) in output. |
1 |
1000 |
3 |
7.3. Compression and extraction¶
7.3.1. starch
¶
Lossless compression of any BED file.
BEDOPS starch documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
1 |
1 |
3 |
|
The internal compression method. The default |
1 |
1 |
3 |
|
Append note to output archive metadata (optional). |
1 |
1 |
3 |
|
Write progress to standard error stream for every N input elements. |
1 |
1 |
3 |
7.3.2. unstarch
¶
Extraction of a
starch
archive or attributes.BEDOPS unstarch documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
1 |
1 |
NA |
|
Show archive’s compression type (either |
1 |
1 |
NA |
|
Show archive version (at this time, either 1.x or 2.x). |
1 |
1 |
NA |
|
Show archive creation timestamp (ISO 8601 format). |
1 |
1 |
NA |
|
Show total, non-unique base counts for optional |
1 |
1 |
NA |
|
Show unique base counts for optional |
1 |
1 |
NA |
|
Decompress information for a single |
1 |
1 |
NA |
|
Report if optional |
1 |
1 |
NA |
|
Show element count for optional |
1 |
1 |
NA |
|
Show element maximum string length for optional |
1 |
1 |
NA |
|
Test if the <starch-file> is a valid starch archive, returning 0/1 for a false/true result |
1 |
1 |
NA |
|
Print the metadata for a |
1 |
1 |
NA |
|
List all chromosomes in |
1 |
1 |
NA |
|
Report if optional |
1 |
1 |
NA |
|
Show descriptive note (if originally added to archive). |
1 |
1 |
NA |
|
Show SHA-1 signature of specified chromosome (Base64-encoded) or all signatures if chromosome is not specified. |
1 |
1 |
NA |
|
Compare SHA-1 signature of specified chromosome with signature that is stored in the archive metadata, reporting error is mismatched. |
1 |
1 |
NA |
7.3.3. starchcat
¶
Merge multiple
starch
archive inputs into onestarch
archive output.BEDOPS starchcat documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
1 |
No imposed limit |
NA |
|
The internal compression method. The default |
1 |
No imposed limit |
NA |
|
Append note to output archive metadata (optional). |
1 |
No imposed limit |
NA |
|
Write progress to standard error stream for every N input elements. |
1 |
No imposed limit |
NA |
7.3.4. starchstrip
¶
Extract or filter a
starch
archive by one or more specified chromosome names.BEDOPS starchstrip documentation.
option |
description |
min. file inputs |
max. file inputs |
min. BED columns |
---|---|---|---|---|
(no option) |
NA |
1 |
No imposed limit |
NA |
|
Writes output with inclusion or exclusion of specified chromosome name records (comma-delimited string). |
NA |
No imposed limit |
NA |