Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/adamtaranto/te-splitter
Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.
https://github.com/adamtaranto/te-splitter
Last synced: 2 months ago
JSON representation
Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.
- Host: GitHub
- URL: https://github.com/adamtaranto/te-splitter
- Owner: Adamtaranto
- License: mit
- Created: 2017-08-15T00:53:39.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2024-11-05T01:30:24.000Z (3 months ago)
- Last Synced: 2024-11-05T02:27:23.322Z (3 months ago)
- Language: Python
- Size: 27.3 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# tSplit the TE-splitter
Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs).
Optionally, compose synthetic MITES from complete DNA transposons.
# Table of contents
* [Algorithm overview](#algorithm-overview)
* [Options and usage](#options-and-usage)
* [Installing tSplit](#installing-tsplit)
* [Example usage](#example-usage)
* [Standard options](#standard-options)
# Algorithm overview
tSplit attempts to identify terminal repeats in transposable elements by
first aligning each element to itself using nucmer, and then applying a set of
tuneable heuristics to select an alignment pair most likely to represent an LTR or TIR.
1. Exclude all diagonal/self-matches
2. If tsplit-LTR: Retain only alignment pairs on the same strand (tandem repeats)
3. If tsplit-TIR: Retain only alignment pairs on opposite strands (inverse repeats)
4. Retain pairs for which the 5' match begins within x bases of element start
and whose 3' match ends within x bases of element end
5. Exclude alignment pairs which overlap (potential SSRs)
6. If multiple candidates remain select alignment pair with largest internal segment
(i.e. closest to element ends)
# Options and usage
### Installing tSplit
Requirements:
* [pymummer](https://pypi.python.org/pypi/pymummer) version >= 0.10.3 with wrapper for nucmer option *--diagfactor*.
* [MUMmer](http://mummer.sourceforge.net/)
* [BLAST+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (Optional)
Installation options:
```bash
# Install from PyPi:
pip install tsplit
# Clone and install from this repository:
git clone https://github.com/Adamtaranto/TE-splitter.git && cd TE-splitter && pip install -e .
```
### Example usage
tSplit contains two programs: tsplit-LTR and tsplit-TIR, for extracting long terminal
repeats and terminal inverted repeats, respectively. Options are the same
for each.
### tsplit-LTR
For each element in *retroelements.fasta* split into internal and external segments.
Split segments will be written to *LTR_split_TE-splitter_output.fasta* with suffix "_I"
for internal or "_LTR" for external segments. LTRs must be at least 10bp in length and
share 80% identity and occur within 10bp of each end of the input element.
```bash
tsplit-LTR -i retroelements.fasta -p LTR_split
```
### tsplit-TIR
For each element in *dna-transposons.fasta* split into internal and external (TIR) segments.
Split segments will be written to *TIR_split_TE-splitter_output.fasta* with suffix "_I" for
internal or "_TIR" for external segments. TIRs must be at least 10bp in length and share 80%
identity and occur within 10bp of each end of the input element. Additionally, synthetic
MITEs will be constructed by concatenation of left and right TIRs, with internal segments
excised.
```bash
tsplit-TIR -i dna-transposons.fasta -p TIR_split --makemites
```
### Standard options
Run `tsplit-LTR --help` or `tsplit-TIR --help` to view the programs' most commonly used
options:
```
Usage: tsplit-[LTR or TIR] [-h] -i INFILE [-p PREFIX] [-d OUTDIR]
[--splitmode {all,split,internal,external,None}]
[--makemites] [--keeptemp] [-v] [-m MAXDIST]
[--minid MINID] [--minterm MINTERM] [--minseed MINSEED]
[--diagfactor DIAGFACTOR] [--method {blastn,nucmer}]
Help:
-h, --help Show this help message and exit.
Input:
-i, --infile Multifasta containing complete elements.
(Required)
Output:
-p, --prefix All output files begin with this string. (Default:[infile basename])
-d, --outdir Write output files to this directory. (Default: cwd)
--keeptemp If set do not remove temp directory on completion.
-v, --verbose If set, report progress.
Report settings:
--splitmode Options: {all,split,internal,external,None}
all = Report input sequence as well as internal and external segments.
split = Report internal and external segments after splitting.
internal = Report only internal segments.
external = Report only terminal repeat segments.
None = Only report synthetic MITES (when --makemites is also set).
(Default: split)
--makemites Attempt to construct synthetic MITE sequences from TIRs by concatenating
5' and 3' TIRs. Available only in 'tsplit-TIR' mode
Alignment settings:
--method Select alignment tool. Note: blastn may perform better on very short high-identity TRs,
while nucmer is more robust to small indels.
Options: {blastn,nucmer}
(Default: nucmer)
--minid Minimum identity between terminal repeat pairs. As float.
(Default: 80.0)
--minterm Minimum length for a terminal repeat to be considered.
Equivalent to nucmer "--mincluster"
(Default: 10)
-m, --maxdist Terminal repeat candidates must be no more than this many bases from ends of an input element.
Note: Increase this value if you suspect that your element is nested within some flanking sequence.
(Default: 10)
--minseed Minimum length of a maximal exact match to be included in final match cluster.
Equivalent to nucmer "--minmatch".
(Default: 5)
--diagfactor Maximum diagonal difference factor for clustering of matches within nucmer,
i.e. diagonal difference / match separation
(default 0.20)
Note: Increase value for greater tolerance of indels between terminal repeats.
```
# License
Software provided under MIT license.