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arbow-0.6.0
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Cultivate your MSA to get better trees
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | arbow-0.6.0 |
| نام | arbow |
| نسخه کتابخانه | 0.6.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Microbiological Diagnostic Unit Public Health Laboratory |
| ایمیل نویسنده | andersgs@gmail.com |
| آدرس صفحه اصلی | https://github.com/MDPHL/arbow |
| آدرس اینترنتی | https://pypi.org/project/arbow/ |
| مجوز | - |
# Arbow: cultivate your multiple sequence aligment to get better trees
  
## Name
We named this tool `arbow` as that would be the phonetic pronounciation of the short, endearing,
term for an [arborist](https://en.wikipedia.org/wiki/Arborist) in Australia.
## What it does
The goal of `arbow` is to automate and simplify the production of trees from multiple sequence alignments. The tool
has been developed in the context of viral phylogenomics.
***NOTE*** SOME DEFAULTS HAVE CHANGED in `v0.6.*`:
- iqtree 2 is assumed by default, with an executable called `iqtree` (these come with new options to set your iqtree environment: `-iv` or `--iqtree-version` to specify the version (either 1 or 2), `-ip` or `--iqtree-path` to specify the path to the executable (assumes `$PATH` by default), and `-ie` or `--iqtree-exec` to define the executable (`iqtree2` by default))
- no sites with missing data are filtered by default (use `-mp` or `-mc` to change this now)
- constant sites are by default those that have 100% of a single base (use `-x` or `-c` to change this)
In the current version (`0.6.*`) it:
1. Reads an alignment in `multiFASTA` format
2. Calculates stats for each sequence in the alignment
3. Trims 5/3 prime UTR regions --- defaults set to SARS-COV-2 (Genbank accession: `NC_045512.2`)
4. Calculates stats per column in the alignment
5. Allows the user to set a threshold of tolerable missing data in a column, and removes all non-conforming columns from the alignment. This can be defined in two ways:
* using the `-mp` flag which defines a proportion of missing sites (e.g., 0.01 means at most 1% missing data)
* using the `-mc` flag which defines the count of missing sites (e.g., 2 means at most 2 missing sites)
* one can still use `-mm` option, but that has been deprecated in favour of the `-mc` option. `-mm` will be removed in version `v0.8.0`.
6. From the remaining columns, `arbow` finds all the `constant` columns according to two `user` defined criteria: `allow missing data` (i.e., a column with missing data can still count to towards `constant` sites if it meets other criteria), and a defined threshold of variation. This process one to smooth over any potential sequencing errors. This threshold can be defined in two ways:
* the frequency of the major allow is equal to or larger than a threshold (i.e., if the threshold is set to 0.99 and there are 100 samples, 99 of which are `A` and one is `G`, that column would be counted as a constant `A`) --- use the `-x` option.
* if the total count of minor alleles is equal to or smaller than a threshold (i.e., if the threshold is 2 and there are 100 samples, 98 of which are `A`, 1 is `C` and 1 is `T`, that column would be considered as a constant `A`) --- use the `-c` option.
7. It then filters out all the `variable` columns, and outputs the variable alignment as a `multiFASTA` alignment.
8. It runs `IQTree` with a few sensible `presets` --- it is now possible to run both IQTree1 and IQTree2.
Currently, in step `4` above, columns that have a single observed `nucleotide` (e.g., `C`) but still have missing data that were not filtered out in step `3` are counted towards the overall frequency of that `base` in the alignment. In other words, if a `user` specifies a maximum number of 20 missing bases, and a column with 5 missing bases but with `A` in all other samples, that column will count towards the overall frequency of `A` in the alignment (i.e., majority consensus imputation). This assumptions is less risky the larger the number of samples in the alignment.
For step `5`, missing data (i.e., `-` and `N`) are all codes as `N`.
Tests are underway to figure out how these assumptions might affect the output.
## Dependencies
1. Python >=3.6
2. IQTree 1.6+ or 2.0.4+
3. BioPython
4. Pandas
5. NumPy
## Installation
### Brew
```
brew install iqtree
pip<3> install arbow
```
### Conda
```
conda install -c bioconda iqtree
pip<3> install arbow
```
## Running
1. Generate a mulitple sequence alignment with your favourite aligner (e.g., MAFTT). Output a `multiFASTA` file.
2. Run `arbow <options> <aln.fa>`
3. Open `tree-YYYY-MM-DD_HHMMSS.treefile` in your favourite tree viewer (e.g, FigTree)
4. Open `tree-YYYY-MM-DD_HHMMSS_bb.treefile` or `tree-YYYY-MM-DD_HHMMSS_alrt.treefile` for branches with `ultra-fast bootstrap` support or `SH-aLRT` support only, respectively.
## Data stream
When running `arbow`, by default a stream is output to the console (`stdout`).
Data about the each sequence in the alignment is prefixed with `[SEQ]`, and is followed by:
1. Count of each base (`A`, `C`, `G`, `T`, and `N` – `N` is any character other than `ACGT`)
2. Percent missing data
3. A status column that has 0, 1, 2, or 3 `*` depending on whether the percent missing data is `<0.5`, `>=0.5 and <1.0`, `>=1.0 and <5.0`, or `>=5`, respectively.
Data about each column in the alignment is prefixed with `[ALN]`, and is followed by:
1. Position in the alignment
2. Count of each base (bases counted will depend on whether all IUPAC codes are allowed or not - see below in usage)
## Command line
## Usage
```
Usage: arbow [OPTIONS] ALN
Options:
--version
-i, --all-iupac Print count of all IUPAC code for column
stats?
-s, --no-stream Stop streaming stats to console
-mm, --max-missing INTEGER Remove sites with 'mm' missing sites or more
[default: 20]
-x, --major-allele-freq FLOAT If major allele frequency is equal or larger
than consider the site constant. [default:
0.99]
-o, --out-var-aln TEXT Filename for alignment of variable sites.
[default: aln-2020-04-07-150443.aln]
-p, --prefix TEXT Prefix to append to IQTree output files.
[default: tree-2020-04-07-150443]
-iv, --iqtree-version [1|2] Version of IQTree to use. [default: 2]
-ip, --iqtree-path PATH Path to iqtree executable
-ie, --iqtree-exec TEXT The IQTree executable [default: iqtree2]
-t, --iqtree-threads INTEGER Number of cores to run IQtree [default: 4]
-m, --iqtree-models TEXT Substitution models to test. [default:
HKY,TIM2,GTR]
-f, --iqtree-freq TEXT Base frequency models to test. [default: F]
-r, --iqtree-rates TEXT Rate category models to test. [default: G,R]
-b, --iqtree-bb INTEGER Maximum number of UltraFast Bootstrap
iterations to attempt. [default: 1000]
-a, --iqtree-alrt INTEGER Number of replicates to perform SH-aLRT.
[default: 1000]
---iqtree-cmax INTEGER Maximum number of rate categories to test.
[default: 5]
-io, --iqtree-outgroup TEXT ID(s) of samples to be used as outgroup in
IQTree. (e.g., single: sample_1, multiple:
'sample_2,sample_3'. This option is ignore
if --use-ref-as-outgroup is selected.
-r, --ref-id TEXT Sequence ID of the reference [default:
MN908947.3]
-u, --use-ref-as-outgroup Use the reference sequence as the outgroup
in IQTree [default: False]
--five-prime-end INTEGER Last base of the 5' UTR region in 1-index in
the ref sequence [default: 265]
--three-prime-start INTEGER First base of the 3' UTR region in 1-index in
the ref sequence [default: 29675]
--include-const When outputting the clean alignment, leave
constant sites in the alignment. [default is
to remove]
-l, --log FILENAME Log file to store output. Use '-' to log to
stdout [default:
arbow-2020-05-05-153619.log]
--help Show this message and exit.
```
## Default behaviour explained
By default, `arbow` will trim the 5' and 3' UTR regions.
### Remove sites with any gaps in the alignment
Let us say that you wish to remove all sites in the alignment that have **any** missing data, and retain all complete columns:
```
arbow -x 1.0 -mc 0 <in.aln>
```
### Keep all sites in an alignment (i.e., skip any filtering)
Let us say that you wish to keep all sites in the alignment, and you have an alignment with 200 sequences:
```
arbow <in.aln>
```
### Keep constant sites in the clean alignment
```
arbow --include-const <in.aln>
```
### Get help
```
arbow <-h|--help>
```
### Get version
```
arbow --version
```
نیازمندی
| مقدار | نام |
|---|---|
| - | pandas |
| - | click |
| - | numpy |
| - | biopython |
| - | scipy |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6, <4 | Python |
نحوه نصب
نصب پکیج whl arbow-0.6.0:
pip install arbow-0.6.0.whl
نصب پکیج tar.gz arbow-0.6.0:
pip install arbow-0.6.0.tar.gz