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توضیحات

Counts file library and conversion scripts.

ویژگی	مقدار
سیستم عامل	-
نام فایل	cflib-pomo-1.3.0.0
نام	cflib-pomo
نسخه کتابخانه	1.3.0.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Dominik Schrempf
ایمیل نویسنده	dominik.schrempf@gmail.com
آدرس صفحه اصلی	https://github.com/pomo-dev/cflib
آدرس اینترنتی	https://pypi.org/project/cflib-pomo/
مجوز	MIT

# Counts file library This python library `cflib` provides scripts to convert between fasta, VCF and counts files. Counts files are used by [PoMo](http://www.cibiv.at/software/iqtree/doc/Polymorphism-Aware-Models/), an implementation of a polymorphism-aware phylogenetic model. We advice you to use PoMo implemented in [IQ-TREE](http://www.cibiv.at/software/iqtree/). For a reference, please see and cite: Schrempf, D., Minh, B. Q., De Maio, N., von Haeseler, A., & Kosiol, C. (2016). Reversible Polmorphism-Aware Phylotenetic Models and their Application to Tree Inference. Journal of Theoretical Biology, in press. # Requirements `cflib` requires [`python` (Version 3.x)](https://www.python.org/) to be installed. `cflib` also uses the following python libraries that will be automatically pulled when installing `cflib`: - [scipy](http://www.scipy.org/), - [numpy](http://www.numpy.org/) and - [pysam](http://code.google.com/p/pysam/). # Installation Install `cflib` and the conversion scripts with ```sh pip install --user cflib-pomo ``` Note that the name of `cflib` on the PyPI repository (which is used by `pip`) is `cflib-pomo`, since the name `cflib` was taken! If the standard Python version of your operation system is still 2.x (e.g., OSX), make sure that you use, `pip3`. The `--user` flag is optional and tells Python to install `cflib` and the scripts only for this user but not system wide. If you want to uninstall `cflib`, ```sh pip uninstall cflib-pomo ``` The [conversion scripts](#Conversion scripts) should be directly available if your `PATH` environment variable is setup correctly. For my Linux installation, the Python path `~/.local/bin` had to be included. This may vary for your operating system. # Example Sample data can be found in [examples](./examples). Assuming that have installed `cflib` we will now convert [`example.fasta`](./examples/example.fasta) to a counts file named `example_from_fasta.cf`. The [script](#conversion-scripts) that we will use is called [`FastaToCounts.py`](./scripts/FastaToCounts.py). First, we have a look at the help message: ```sh FastaToCounts.py --help ``` usage: FastaToCounts.py [-h] [-v] [--iupac] fastaFile output Convert fasta to counts format. The (aligned) sequences in the fasta file are read in and the data is written to a counts format file. Sequence names are stripped at the first dash. If the stripped sequence name coincide, individuals are put into the same population. E.g., homo_sapiens-XXX and homo_sapiens-YYY will be in the same population homo_sapiens. Take care with large files, this uses a lot of memory. The input as well as the output files can additionally be gzipped (indicated by a .gz file ending). If heterozygotes are encoded with IUPAC codes (e.g., 'r' for A or G), homozygotes need to be counted twice so that the level of polymorphism stays correct. This can be done with the `--iupac` flag. positional arguments: fastaFile path to (gzipped) fasta file output name of (gzipped) outputfile in counts format optional arguments: -h, --help show this help message and exit -v, --verbose turn on verbosity (-v or -vv) --iupac heteorzygotes are encoded with IUPAC codes As requested, the sequence names in `example.fasta` are, e.g., `Sheep-1`, `Sheep-2`, and so on. The following code converts the file `example.fasta` into the counts file `example_from_fasta.cf`: ```sh FastaToCounts.py example.fasta example_from_fasta.cf ``` # Note on IUPAC codes IUPAC codes are supported and handled adequately. In particular, - `N` can be used to denote any base or that the base is unknown; the letter `*` can also be used in this case, although it is non-standard; - `-` or `.` denote a gap or a deletion. Also the other IUPAC codes are supported. # Conversion scripts - [CountsToFasta.py](./scripts/CountsToFasta.py): Convert a counts file to a fasta file. - [FastaToCounts.py](./scripts/FastaToCounts.py): Convert a fasta file to counts format. - [FastaToVCF.py](./scripts/FastaToVCF.py): Convert a fasta file to variant call format. - [FastaVCFToCounts.py](./scripts/FastaVCFToCounts.py): Convert a fasta reference with VCF files to counts format. - [FilterMSA.py](./scripts/FilterMSA.py): Filter a multiple sequence alignment file (apply standard filters; cf. `libPoMo`). - [GPToCounts.py](./scripts/GPToCounts.py): Experimental. Convert gene prediction files with reference to counts format. - [MSAToCounts.py](./scripts/MSAToCounts.py): Convert multiple sequence alignments with VCF files to counts format. Each script comes with its own documentation. Please execute, e.g., ```sh FastaToCounts.py --help ``` All conversion scripts can be found in the [scripts](./scripts) folder. # Documentation If you are interested in `cflib` itself, please refer to the [cflib reference manual](http://cflib.readthedocs.io/en/latest/).

نیازمندی

مقدار	نام
-	scipy
-	numpy
-	pysam

نحوه نصب

نصب پکیج whl cflib-pomo-1.3.0.0:

pip install cflib-pomo-1.3.0.0.whl

نصب پکیج tar.gz cflib-pomo-1.3.0.0:

pip install cflib-pomo-1.3.0.0.tar.gz