semvec/pypi-packages huggingface dataset:
extract-codon-alignment 0.0.1
To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.
Requires Python: >=3

# extract-codon-alignment

## 1 Introduction

`extract-codon-alignment`  (https://github.com/linzhi2013/extract_codon_alignment) is a tool to extract some codon positions (1st, 2nd, 3rd) from a CDS alignment with `Biopython` (http://www.biopython.org/)

## 2 Installation

    $ pip install extract-codon-alignment
    # or with Bioconda
    conda install extract-codon-alignment

There will be a command `extract_codon_alignment` created under the same directory as your `pip` command.

## 3 Usage

    $ extract_codon_alignment
    usage: extract_codon_alignment [-h] --alignedCDS <file>
                                   [--aln_format <format>]
                                   [--codonPoses {1,2,3,12,13,23}] --outAln <file>

    To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.

    optional arguments:
      -h, --help            show this help message and exit
      --alignedCDS <file>   The CDS alignment.
      --aln_format <format>
                            the file format for the CDS alignment. Anything
                            accepted by BioPython is fine [fasta]
      --codonPoses {1,2,3,12,13,23}
                            Codon position(s) to be extracted [12]
      --outAln <file>       output file name

## Author
Guanliang MENG

## Citation
Currently I have no plan to publish `extract-codon-alignment`.

However, since `extract-codon-alignment` makes use of `Biopython`, you should cite it if you use `extract-codon-alignment` in your work:

    Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163

Please go to `http://www.biopython.org/` for more details.
timeship 1.0.1
Easy timing of all kinds of python code.

# Timeship

The timeship lets you easily and transparently time execution times within your python code.

Its concept is that you set anchors in your code specifying timing routes. The timeship module will time the specified routes and transparently inform you about their execution time.

## installation
Timeship can be installed using `pip` via:
```bash
pip install timeship
```

## demo
Simply execute the following python snippet to see the timeship on sea!
```python
import time
from timeship import timeship


with timeship.Anchor("BuildShip"):
    with timeship.Anchor("CollectMaterial"):
        time.sleep(0.2)
    with timeship.Anchor("CarftHull"):
        time.sleep(0.3)
    with timeship.Anchor("CraftMast"):
        time.sleep(0.4)
        with timeship.Anchor("HoistSail"):
            time.sleep(0.1)

with timeship.Anchor("Sail"):
    time.sleep(0.6)

timeship.plot("timeship_demo")

```

## usage
You have two basic different options to set anchors

### the anchor function
The fist option is using timeships anchor function as follows:
```python
# set anchor Arrr
timeship.anchor("Arrr")
# execute code
time.sleep(0.1)
# release anchor Arrr
timeship.anchor("Arrr", release=True)

# set anchor Orrr
timeship.anchor("Orrr")
# execute some code
time.sleep(0.4)
# additionally set anchor Errr
timeship.anchor("Errr")
# execute some other code
time.sleep(0.4)
# release all active anchors by not specifying a name
timeship.anchor()
```

### contexts
The second option is to use contexts

```python
with timeship.Anchor("setup"):
    time.sleep(0.1)
```

### nesting
The timeship also supports nested contexts.
Nested timing context can be specified using a slashy (`context/subcontext`) notation:
```python
timeship.anchor("xdata/load")
time.sleep(0.1)
timeship.anchor()
timeship.anchor("xdata/augment")
```

or by nesting contexts:
```python
with timeship.Anchor("ydata"):
    with timeship.Anchor("load"):
        # execute ydata loading code
        time.sleep(0.2)
    with timeship.Anchor("augment"):
        # execute ydata augmentation code
        time.sleep(0.3)
```

or equivalently:
```python
with timeship.Anchor("zdata/load"):
    # execute zdata loading code
    time.sleep(0.2)
with timeship.Anchor("zdata/augment"):
    # execute zdata augmentation code
    time.sleep(0.3)
```

## plotting timing data
At the end of your code, plot the results by by using the `plot` function. Timeships plotting function (`timeship.plot()`) creates a directory (specified by the `dir` argument) with an index.html containing a d3 plot with the timing data which can be viewed through a webbrowser.

```python
timeship.plot(dir="timeship")
```
This will create a new directory (in this case called "timeship") and store an html page, which contains a clear visualization of the timing data.

Sail on through space and time, Arrr!