PyOmiX - Analysis Workflow

Analysis Workflow Course Project - Programming for Bioinformatics (Bioinformatics Professional Diploma)

GROUP MEMBERS:

• Ahmed Omar Lamloum
• Mohamed Magdy AboelEla (Team Leader)
• Usama Bakry
• Waleed Faheem Amer

OVERVIEW:

The overall purpose of PyOmiX is to create an analysis workflow that generate a simple phylogeny trees from multiple sequence alignment files for a list of SWISS-Prot ids using Clustal Omega, throughout a series of steps as described in the following flowchart.

INPUTS:

python pyomix.py -i <swiss-prot ids file dir> -d <database fasta file> -o <output dir>

OUTPUTS:

• Directory with a subdirectory for each ID from the input list.
• In each directory:
  • Sequence fasta file from UniProt.
  • Alignment file from Diamond.
  • Sequences fasta file for accessions numbers from NCBI.
  • Mulitple sequence alignment file from Clustal Omega.
  • Phylogenetic tree from Clustal Omega.

SUBTASKS:

1. Function to make directories for swiss-prot ids. (done)
   • Input: ids file.
   • Output: list of ids directories.
2. Function to get fasta file (sequence) using request from UniProt.
   • Input: swiss-prot id.
   • Output: sequence fasta file.
3. Function to align sequence using Diamond. (done)
   • Input: sequence fasta file and database file.
   • Output: alignment file.
4. Function to get fasta file (sequence) using request from NCBI.
   • Input: accession number.
   • Output: sequence fasta file.
5. Function to merge multiple fasta files in one fasta file.
   • Input: list of fasta files.
   • Output: fasta file.
6. Function to perform multiple sequence alignment and get a phylogenetic tree.
   • Input: fasta file.
   • Output: alignment file and phylogenetic tree file.
7. Implement python script to run it on the command line.

EXTERNAL MODULES AND PROGRAMMES TO BE USED:

1. Diamond Aligner.
2. Clustal Omega (clustalo.py)

EXPECTED DIFFICULTIES:

1. Unsuitability of the extracted phylogenetic tree from Clustal Omega, so, we will use Simple Phylogeny Tree module instead.
2. Implementation the python script to run it on command line.

TASKS TO BE COMPLETED BY THE 4TH OF MAY:

1. Function to make directories for swiss-prot ids. (done)
2. Function to get fasta file (sequence) using request from UniProt.
3. Function to align sequence using Diamond. (done)
4. Function to get fasta file (sequence) using request from NCBI.