https://github.com/gedankenstuecke/cluster-pipline

https://github.com/gedankenstuecke/cluster-pipline

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• Host: GitHub
• URL: https://github.com/gedankenstuecke/cluster-pipline
• Owner: gedankenstuecke
• Created: 2012-06-25T11:49:22.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2012-09-05T11:32:30.000Z (over 12 years ago)
• Last Synced: 2024-11-13T14:25:42.080Z (2 months ago)
• Language: Python
• Size: 652 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# Clustering pipeline

A small collection of scripts to perform clustering of transcriptome-sequences.

## Goals

* Predict open reading frames (ORFs) from transcriptome contigs using blast-hits as guidance

* Cluster orthologous ORFs of different species together

* Create peptide & nucleotide-alignments from those clusters

## Dependencies

* (Bio)python for the pipeline itself

* OrthoMCL v2.0, which needs 

** MySQL

** blastall-package

* Perl to run the protein2nucleotide-alignment-script

## Usage

In short:

* Run Clustr.py and wait

In detail:

* Clustr.py will try to find a file named "config.cfg" to get all the settings, an example is _config.cfg.example_ (surprise!). You can also specify the config-file using the _"-c"_ parameter while starting: `Clustr.py -c /some/config/somewhere.cfg`

* In the config-file you will have to provide (looking at the example should give you an idea): 

    * The organisms/assemblies you want to cluster

    * You can choose to skip the ORF prediction if you already have protein- & nucleotide-sequences for the ORFs

        * In this case: Specify the nucleotide-ORF-fasta as *assembly_fasta* and the protein-ORF-fasta as *peptides_fasta*

    * If you want to perform the ORF prediction: Where the blastx-supported protein-blast-database is located you want to use for the ORF-prediction

    * Where your makeblastdb-binary and the OrthoMCL-binaries are located

    * The credentials for your MySQL-database (write & delete-access is required)

    * Some output-details for OrthoMCL (name of the resulting clusters etc.)

    * After setting up your config: Run Clustr.py

## To-Do

* Implement further trimming of resulting alignments

* Implement analysis of resulting alignments

## Known bugs

* Sometimes the nucleotide-sequences, given by the ORF-prediction, are longer than the corresponding protein-sequences. Due to this the protein2nucleotide-alignment won't work. Probably a bug in the orf-prediction-scripts.