sample_example

Toy example

Here we present a walkthrough of running make_prg on a toy example. We run:

1. make_prg from_msa to create PRGs from MSAs;
2. make_prg update to update PRGs with denovo paths;

Note: there is no need to have make_prg itself installed. The test script downloads the precompiled binary of the latest release.

Input data description

msas/ : contains the MSAs of 2 genes we are using as toy example here;
denovo_paths/denovo_paths.txt : contains some denovo paths on these 2 genes. This file is produced by pandora;

Running

./run_make_prg_on_sample_example.sh

Quick look at the output

Output files from make_prg from_msa:

1. msas_output/sample.prg.fa: contains the PRGs built from the MSAs in fasta format;
2. msas_output/sample.prg.bin.zip: contains the PRGs built from the MSAs in a binary format;
3. msas_output/sample.prg.gfa.zip: contains the GFA representation of the PRGs;
4. msas_output/sample.update_DS.zip: contains data structures that make the PRGs updatable;

Output files from make_prg update:

The output files from make_prg update are identical to make_prg from_msa, except that the PRGs are updated with respect to the variants described in denovo_paths/denovo_paths.txt

Checking the denovo variants added to the graph

Diffing msas_output/sample.prg.fa and msas_updated/updated_sample.prg.fa, we can see that the updated PRGs have more sites/alleles:

$ diff msas_output/sample.prg.fa msas_updated/updated_sample.prg.fa 
2c2
< TTGAGTAAAACAATCCCCCGCGCTTATATAAGCGCGTTGATATTTTTAATTATTAACAAGCAACATCATGCTAATACAGACATACAAGGAGATCATCTCTCTTTGCCTGTTTTTTATTATTTCAGGAGTGTAAACACATTTTCCG 5 T 6 C 5 CTCCCTGGCTAAT 7 C 8 A 7 ACCACATTGGCATTTATGGAGCACATCACAATATTTCAATACCATTAAAGCACTGCA 9 C 10 T 9 CAAAATGAAACACTGCGA 11 C 12 T 11 ATTAAAATT 13 A 14 C 13 TTTCAATT
---
> TTGAGTAAAACAATCCCCCGCGCTTATATAAGCGCGTTGATATTTTTA 5 A 6 G 5 TTATTAACAAGCAACATCATGCTAATACAGACATACAAGGAGATCATCTCTCTTTGCCTGTTTTTTATTATTTCAGGAGTGTAAACACATTTTCCG 7 T 8 C 7 CTCCCTGGCTAAT 9 C 10 A 9 ACCACATTGGCATTTATGGAGCACATCACAATATTTCAATACCATTAAAGCACTGCA 11 C 12 T 11 CAAAATGAAACACTGCGA 13 C 14 T 13 ATTAAAATT 15 A 16 C 15 TTTCAATT
4c4
< ATGCAGATACGTGAACAGGGCCGCAAAATTCAGTGCATCCGCACCGTGTACGACAAGGCCATTGGCCGGGGTCGGCAGACGGTCATTGCCACACTGGCCCGCTATACGAC 5 C 6 G 5 GAAATGCCCACGACCGGGCTGGATGAGCTGACAGAGGCCGAACGCGAGAC 7 A 8 G 7 CTGGCCGAATGGCTGGCCAAGCGCCGGGAAGCCTCGCAGAAGTCGCAGGAGGCCTACACGGCCATGTCTGCGGATCGGTGGCTGGTCACGCTGGCCAAGGCCATCAGGGAAGGGCAGGA 9 GCTA 10 ACTG 9 CGCCCCGAACAGGCGGCCGCGATCTGGCACGGCATGGGGGA 11 A 12 G 11 GTCGGCAAGGCCTTGCGCAAGGCTGGTCACGCGAAGCCCAAGGCGGTCAGAAAGGGCAAGCCGGTCGATCCGGCTGATCCCAAGGATCAAGGGGAGGGGGCACCAAAGGGGAAATGA
---
> ATGCAGATACGTGAACAGGGCCGCAAAATTCAGTGCATCCGCA 5 C 6 T 5 CGTGTACGACAAGGCCATTGGCCGGGGTCGGCAGACGGTCATTGCCACACTGGCCCGCTATACGAC 7 C 8 G 7 GAAATGCCCACGACCGGGCTGGATGAGCTGACAGAGGCCGAACGCGAGAC 9 A 10 G 9 CTGGCCGAATGGCTGGCCAAGCGCCGGGAAGCCTCGCAGAAGTCGCAGGAGGCCTACACGGCCATGTCTGCGGATCGGTGGCTGGTCACGCTGGCCAAGGCCATCAGGGAAGGGCAGGA 11 GCTA 12 ACTG 11 CGCCCCGAACAGGCGGCCGCGATCTGGCACGGCATGGGGGA 13 A 14 G 13 GTCGGCAAGGCCTTGCGCAAGGCTGGTCACGCGAAGCCCAAGGCGGTCAGAAAGGGCAAGCCGGTCGATCCGGCTGATCCCAAGGATCAAGGGG 15 A 16 T 15 GGGGGCACCAAAGGGGAAATGA