MCScanx-python-wrapper

This is a python wrapper for running MCScanx

MCScanX is an amazing tool for identifying and visualyzing syntenic blocks between two or more genomes. Unfortunately, the first time I ran it I had a lot of issues, and the manual could be better. So, I decided to write this python wrapper.

Before running the wrapper, the following tools must be installed and available in the path:

• blastp (and makeblastdb)
• python 3 or higher (tested on 3.8.12)
• Biopython
• MCScanX directory must be in the working directory and installed. Installation is very simple following the developer's instructions.
• The wrapper installation is not needed, just download the code and is ready to be used.

All of the dependencies can be easily installed using developer's instructions or conda.

Input data:

• Genome references must be in fasta format. Chromosome names must contain 2 letters and one number (i.e ch1, ch2, ch3, etc)
• Genome annotations must be in gff/gff3 format (gene id must be indicated in the 8th column and with the following format: ID=). The chromosome name/ID must match the gff.

Now, you're ready to run it!

Ussage of the wrapper:

python macscanxWrapper.py -h 
usage: macscanxWrapper.py [-h] -f1 specie1.fasta -g1 specie1.gff -f2 file2.fasta -g2 specie2.gff -t threads(int) -p prefix

	Python wrapper for MCScanX
---------------------
Tested on python 3.8.12

optional arguments:
  -h, --help            show this help message and exit

Mandatory arguments:
  -f1  --fasta1          Fasta file for specie1 (Genomic sequence)
  -g1  --gff1            GFF/GFF3 file for specie1
  -f2  --fasta2          Fasta file for specie2 (Genomic sequence)
  -g2  --gff2            GFF/GFF3  file for specie2
  -t   --blastp_threads  Number of threads (CPUs) to use in the BLAST search
  -p   --prefix          Job prefix, it will be used for MCScanX results

The pipeline:

Step 1. Checking dependencies

The first step is to check all dependencies are in the correct path and/or running.

Step 2. Loading/parsing input data

• By default, only gene features will be extracted.
• By default the standard code (table 1) is used for protein translation.
• Pseudogenes (missing any start codon) will be ignored.
• MCScanX needs a bed-like file containing the annotation (with the following format: chr\tgeneID\tStart\tEnd), it is created and named as prefix.gff (please notice it is not a conventional gff file, but is used for visualization i.e using SynVisio).

Step 3. Running blastp and MCScanX

• Proteins from species1 and species2 will be merged into a single file. If you want to compare >2 species, there is no need to duplicate them in the input data, they can be present either in species1 or species2.
• By default, blastp will only keep the 5 matches for every sequence in the query.
• The number of threads for running blastp must be specified (reccomended >= 15).
• MCScanX will run in its own directory.

Step 4. Output files

• Output files from MCScanX will be placed in the working directory.

Running the wrapper using test files:

python macscanxWrapper.py -f1 g3_test.fasta -g1 g3_test.gff3 -f2 3688_test.fasta -g2 3688_test.gff3 -t 15 -p test_final

Checking dependencies... 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
./MCScanX-master directory is ready...
./MCScanX is ready...
blastp command is ready...
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

Loading and parsing input files...

Valid sequences (proteins) in g3_test.fasta: 11195
Valid Sequences (proteins) in 3688_test.fasta: 10999
Annotation file ready: test_final.gff

Generate blastdb:
makeblastdb -in species_merged.faa -dbtype prot
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 


Building a new DB, current time: 03/29/2023 12:52:37
New DB name:   /Users/Documents/python_wrapperMCScanX/species_merged.faa
New DB title:  species_merged.faa
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 22194 sequences in 0.444309 seconds.
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

Running Blastp:
blastp -query species_merged.faa -db species_merged.faa -outfmt 6 -out test_final.blast -max_hsps 5 -max_target_seqs 5 -num_threads 15
Files for MCScanX are ready: test_final.blast, test_final.gff

MCScanX is running ... 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
Reading BLAST file and pre-processing
Generating BLAST list
66695 matches imported (40987 discarded)
3 pairwise comparisons
249 alignments generated
Pairwise collinear blocks written to test_final.collinearity [2.978 seconds elapsed]
Tandem pairs written to test_final.tandem
Writing multiple syntenic blocks to HTML files
tv1.html
vt1.html
Done! [0.582 seconds elapsed]
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
MCScanX finished succesfully ... 

Output files

• test_final.blast
• test_final.collinearity
• test_final.gff
• test_final.html (directory)
• test_final.tandem