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Bedtools_Intersect (#94)
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* Initial Commit

* Update config.vsh.yaml

* creating templates

* Update config.vsh.yaml

* Update script.sh

* Added output

* Update config.vsh.yaml

* Update test.sh

* Update test.sh

* More tests

* small changes

* update

- change some var names
- debugged
- added more test

* Update CHANGELOG.md

* Update

* Update help.txt
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tgaspe authored Jul 31, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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* `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).

* `bedtools`:
- `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

## MINOR CHANGES

* `busco` components: update BUSCO to `5.7.1` (PR #72).
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255 changes: 255 additions & 0 deletions src/bedtools/bedtools_intersect/config.vsh.yaml
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name: bedtools_intersect
namespace: bedtools
description: |
bedtools intersect allows one to screen for overlaps between two sets of genomic features.
Moreover, it allows one to have fine control as to how the intersections are reported.
bedtools intersect works with both BED/GFF/VCF and BAM files as input.
keywords: [feature intersection, BAM, BED, GFF, VCF]
links:
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
repository: https://github.com/arq5x/bedtools2
references:
doi: 10.1093/bioinformatics/btq033
license: GPL-2.0, MIT
requirements:
commands: [bedtools]
authors:
- __merge__: /src/_authors/theodoro_gasperin.yaml
roles: [ author, maintainer ]

argument_groups:
- name: Inputs
arguments:
- name: --input_a
alternatives: -a
type: file
direction: input
description: |
The input file (BED/GFF/VCF/BAM) to be used as the -a file.
required: true
example: input_a.bed

- name: --input_b
alternatives: -b
type: file
direction: input
multiple: true
description: |
The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).
required: true
example: input_b.bed

- name: Outputs
arguments:
- name: --output
type: file
direction: output
description: |
The output BED file.
required: true
example: output.bed

- name: Options
arguments:
- name: --write_a
alternatives: -wa
type: boolean_true
description: Write the original A entry for each overlap.

- name: --write_b
alternatives: -wb
type: boolean_true
description: |
Write the original B entry for each overlap.
Useful for knowing _what_ A overlaps. Restricted by -f and -r.
- name: --left_outer_join
alternatives: -loj
type: boolean_true
description: |
Perform a "left outer join". That is, for each feature in A report each overlap with B.
If no overlaps are found, report a NULL feature for B.
- name: --write_overlap
alternatives: -wo
type: boolean_true
description: |
Write the original A and B entries plus the number of base pairs of overlap between the two features.
- Overlaps restricted by -f and -r.
Only A features with overlap are reported.
- name: --write_overlap_plus
alternatives: -wao
type: boolean_true
description: |
Write the original A and B entries plus the number of base pairs of overlap between the two features.
- Overlaps restricted by -f and -r.
However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.
- name: --report_A_if_no_overlap
alternatives: -u
type: boolean_true
description: |
Write the original A entry _if_ no overlap is found.
- In other words, just report the fact >=1 hit was found.
- Overlaps restricted by -f and -r.
- name: --number_of_overlaps_A
alternatives: -c
type: boolean_true
description: |
For each entry in A, report the number of overlaps with B.
- Reports 0 for A entries that have no overlap with B.
- Overlaps restricted by -f and -r.
- name: --report_no_overlaps_A
alternatives: -v
type: boolean_true
description: |
Only report those entries in A that have _no overlaps_ with B.
- Similar to "grep -v" (an homage).
- name: --uncompressed_bam
alternatives: -ubam
type: boolean_true
description: Write uncompressed BAM output. Default writes compressed BAM.

- name: --same_strand
alternatives: -s
type: boolean_true
description: |
Require same strandedness. That is, only report hits in B.
that overlap A on the _same_ strand.
- By default, overlaps are reported without respect to strand.
- name: --opposite_strand
alternatives: -S
type: boolean_true
description: |
Require different strandedness. That is, only report hits in B
that overlap A on the _opposite_ strand.
- By default, overlaps are reported without respect to strand.
- name: --min_overlap_A
alternatives: -f
type: double
description: |
Minimum overlap required as a fraction of A.
- Default is 1E-9 (i.e., 1bp).
- FLOAT (e.g. 0.50)
example: 0.50

- name: --min_overlap_B
alternatives: -F
type: double
description: |
Minimum overlap required as a fraction of B.
- Default is 1E-9 (i.e., 1bp).
- FLOAT (e.g. 0.50)
example: 0.50

- name: --reciprocal_overlap
alternatives: -r
type: boolean_true
description: |
Require that the fraction overlap be reciprocal for A AND B.
- In other words, if -f is 0.90 and -r is used, this requires
that B overlap 90% of A and A _also_ overlaps 90% of B.
- name: --either_overlap
alternatives: -e
type: boolean_true
description: |
Require that the minimum fraction be satisfied for A OR B.
- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
that either 90% of A is covered OR 10% of B is covered.
Without -e, both fractions would have to be satisfied.
- name: --split
type: boolean_true
description: Treat "split" BAM or BED12 entries as distinct BED intervals.

- name: --genome
alternatives: -g
type: file
description: |
Provide a genome file to enforce consistent chromosome
sort order across input files. Only applies when used
with -sorted option.
example: genome.txt

- name: --nonamecheck
type: boolean_true
description: |
For sorted data, don't throw an error if the file
has different naming conventions for the same chromosome
(e.g., "chr1" vs "chr01").
- name: --sorted
type: boolean_true
description: |
Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
- name: --names
type: string
description: |
When using multiple databases, provide an alias
for each that will appear instead of a fileId when
also printing the DB record.
- name: --filenames
type: boolean_true
description: When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.

- name: --sortout
type: boolean_true
description: When using multiple databases, sort the output DB hits for each record.

- name: --bed
type: boolean_true
description: If using BAM input, write output as BED.

- name: --header
type: boolean_true
description: Print the header from the A file prior to results.

- name: --no_buffer_output
alternatives: --nobuf
type: boolean_true
description: |
Disable buffered output. Using this option will cause each line
of output to be printed as it is generated, rather than saved
in a buffer. This will make printing large output files
noticeably slower, but can be useful in conjunction with
other software tools and scripts that need to process one
line of bedtools output at a time.
- name: --io_buffer_size
alternatives: --iobuf
type: integer
description: |
Specify amount of memory to use for input buffer.
Takes an integer argument. Optional suffixes K/M/G supported.
Note: currently has no effect with compressed files.
resources:
- type: bash_script
path: script.sh

test_resources:
- type: bash_script
path: test.sh

engines:
- type: docker
image: debian:stable-slim
setup:
- type: apt
packages: [bedtools, procps]
- type: docker
run: |
echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
runners:
- type: executable
- type: nextflow
119 changes: 119 additions & 0 deletions src/bedtools/bedtools_intersect/help.txt
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```bash
bedtools intersect
```

Tool: bedtools intersect (aka intersectBed)
Version: v2.30.0
Summary: Report overlaps between two feature files.

Usage: bedtools intersect [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>

Note: -b may be followed with multiple databases and/or
wildcard (*) character(s).
Options:
-wa Write the original entry in A for each overlap.

-wb Write the original entry in B for each overlap.
- Useful for knowing _what_ A overlaps. Restricted by -f and -r.

-loj Perform a "left outer join". That is, for each feature in A
report each overlap with B. If no overlaps are found,
report a NULL feature for B.

-wo Write the original A and B entries plus the number of base
pairs of overlap between the two features.
- Overlaps restricted by -f and -r.
Only A features with overlap are reported.

-wao Write the original A and B entries plus the number of base
pairs of overlap between the two features.
- Overlapping features restricted by -f and -r.
However, A features w/o overlap are also reported
with a NULL B feature and overlap = 0.

-u Write the original A entry _once_ if _any_ overlaps found in B.
- In other words, just report the fact >=1 hit was found.
- Overlaps restricted by -f and -r.

-c For each entry in A, report the number of overlaps with B.
- Reports 0 for A entries that have no overlap with B.
- Overlaps restricted by -f, -F, -r, and -s.

-C For each entry in A, separately report the number of
- overlaps with each B file on a distinct line.
- Reports 0 for A entries that have no overlap with B.
- Overlaps restricted by -f, -F, -r, and -s.

-v Only report those entries in A that have _no overlaps_ with B.
- Similar to "grep -v" (an homage).

-ubam Write uncompressed BAM output. Default writes compressed BAM.

-s Require same strandedness. That is, only report hits in B
that overlap A on the _same_ strand.
- By default, overlaps are reported without respect to strand.

-S Require different strandedness. That is, only report hits in B
that overlap A on the _opposite_ strand.
- By default, overlaps are reported without respect to strand.

-f Minimum overlap required as a fraction of A.
- Default is 1E-9 (i.e., 1bp).
- FLOAT (e.g. 0.50)

-F Minimum overlap required as a fraction of B.
- Default is 1E-9 (i.e., 1bp).
- FLOAT (e.g. 0.50)

-r Require that the fraction overlap be reciprocal for A AND B.
- In other words, if -f is 0.90 and -r is used, this requires
that B overlap 90% of A and A _also_ overlaps 90% of B.

-e Require that the minimum fraction be satisfied for A OR B.
- In other words, if -e is used with -f 0.90 and -F 0.10 this requires
that either 90% of A is covered OR 10% of B is covered.
Without -e, both fractions would have to be satisfied.

-split Treat "split" BAM or BED12 entries as distinct BED intervals.

-g Provide a genome file to enforce consistent chromosome sort order
across input files. Only applies when used with -sorted option.

-nonamecheck For sorted data, don't throw an error if the file has different naming conventions
for the same chromosome. ex. "chr1" vs "chr01".

-sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.

-names When using multiple databases, provide an alias for each that
will appear instead of a fileId when also printing the DB record.

-filenames When using multiple databases, show each complete filename
instead of a fileId when also printing the DB record.

-sortout When using multiple databases, sort the output DB hits
for each record.

-bed If using BAM input, write output as BED.

-header Print the header from the A file prior to results.

-nobuf Disable buffered output. Using this option will cause each line
of output to be printed as it is generated, rather than saved
in a buffer. This will make printing large output files
noticeably slower, but can be useful in conjunction with
other software tools and scripts that need to process one
line of bedtools output at a time.

-iobuf Specify amount of memory to use for input buffer.
Takes an integer argument. Optional suffixes K/M/G supported.
Note: currently has no effect with compressed files.

Notes:
(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist,
and excluded if an overlap cannot be found. If multiple overlaps exist, they are not
reported, as we are only testing for one or more overlaps.




***** ERROR: No input file given. Exiting. *****
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