FastaTransformer 0.0.14

This package helps resolve bioprogramming problems

FastaTransformer

FastaTransformer is a python toolset containing fucntions to simplify the usage of .fasta files in analysis as well as transform them into useful states for other tools.

Authors

The primary author of the FastaTransformer package is MDinhobl.

Major Functions

The following list contains the most useful functions of FastaTransformer.

Creating Data Folders

1. MakeGeneBank - Take a CSV or pandas Dataframe with columns representing Genomes, Gene (or other category), and Sequence and create a folder of .fasta files for each Gene (or chosen category).
2. GeneBankToAlignmentBank - Uses Muscle (must be installed locally) to transform a folder of .fasta files into a folder of matching alignment files.
3. AlignmentBankToMatrixBank - Take a folder of .fasta alignment files (such as one produced by GeneBankToAlignmentBank) and produce a folder of distance matricies using the BioPython package.
4. MatrixBankToClusterBank - Take a folder of distance matricies and create a folder of clusters using DBSCAN.

The functionality of the above tools are combined in CSVToAllBanks - A tool that combines the functionality of MakeGeneBank, GeneBankToAlignmentBank, AlignmentBankToMatrixBank, and MatrixBankToClusterBank into one script.

Other Tools

1. AlignmentChangeFinder - Searches a folder of .fasta alignment files for novel changes in several designated ('new') genomes compared to reference ('old') genomes. These results can be further refined by AlignmentChangeFinderCleanup.
2. MatrixBankToAverageMatrix - Take a folder of distance matricices and produce an 'average' distance matrix with weights.
3. MatrixBankStats - Find the statistics of each gene in a folder of distance matricies, such as one produced by AlignmentBankToMatrixBank.
4. FastaDescriptionHunter - A tool used to search the descriptions of fasta entries (everything following the ">") downloaded from the NCBI Genbank for information in specific categories. This is especially useful when trying to search for speicfic sequences after gathering a large number of accession sequences, such as when using NCBI Batch Entrez.

Installation

To install the latest version of FastaTransformer, use pip install:

pip install FastaTransformer

What is a .fasta file?

A .fasta file is a text file format commonly used for storing sequence information for genomic analysis. Each .fasta file can contain information on multiple sequences. Each sequence includes the following information:

• The first row consists of an ">" followed by a sequence id and possibly a description.
• The next row (or rows) contain the sequence itself. It can either be an amino acid sequence or a nucleotide sequence.

Here is an example of text within a .fasta file with three sequences, two of which include a description:

>Genome1
ATATGCAC
>Genome2 [Gene = B602L]
ATATGCAT
>Genome2 [Gene = P72]
ATATGCATC

Documentation for .fasta files can be found at the NCBI and general examples provided at Wikipedia as well as Bioinformatics.nl.