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https://github.com/jherrero/oxford-plots
eHive pipeline to build pairwise Oxford plots
https://github.com/jherrero/oxford-plots
Last synced: 4 months ago
JSON representation
eHive pipeline to build pairwise Oxford plots
- Host: GitHub
- URL: https://github.com/jherrero/oxford-plots
- Owner: jherrero
- Created: 2014-12-03T11:50:20.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2019-08-11T21:44:42.000Z (almost 5 years ago)
- Last Synced: 2024-01-17T03:18:26.287Z (6 months ago)
- Language: Perl
- Size: 1.31 MB
- Stars: 11
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Lists
- repo-5916-awesome-genome-visualization - oxford-plots - plots/blob/master/examples/pig_X_Y.txt) [(img)](https://cmdcolin.github.io/awesome-genome-visualization/oxford.png) (Dotplot)
- awesome-genome-visualization - oxford-plots
README
OxfordPlots
===========
This software is intended to build pairwise dotplots (also known as Oxford plots) for a set of
species vs one particular reference genome. It can be used for just a pair of species or just a
sub-set of chromosomes (instead of using whole genomes).
Usage
=====
This has been developed as an eHive pipeline (see https://github.com/Ensembl/ensembl-hive). Firstly,
you need to download the (soft-masked) sequences, one chromosome per file, one species per
directory. You also need to pre-calculate the length of each chromosome and store this in a text
file.
Please refer to the PerlDoc of src/OxfordPlots.pm for furhter details on the options.
Full Example
============
Organise your input
-------------------
```
# Create the input directory (called "genomes" by default)
mkdir genomes
cd genomes
# Download the files from Ensembl (for this example, we will use only chr1 and chr2 from human and chimp)
../src/download_ensembl_genome.pl --species homo_sapiens --release 77 --chr 1 --chr 2
../src/download_ensembl_genome.pl --species pan_troglodytes --release 77 --chr 1 --chr 2A --chr 2B
gunzip */*.fa.gz
# Get the length of the chromosomes:
rm -f *.txt;
ls -d1 * | while read dir; do perl -lne '
if (/^>(\S+)/) {
if ($name) {
print "$name\t$l"
};
$name = $1;
$l = 0;
next
} $l += length($_);
END {print "$name\t$l"}
' $dir/*.fa >> $dir.txt; done
# Run faToNib on each file (naming the nib file according to the sequence name, not the file name)
ls */*.fa | perl -lne '
my $dir = $_;
$dir =~ s/\/[^\/]*$//;
my $name = qx"head -n 1 $_";
$name =~ s/^>(\S+).*/$1/;
chomp($name);
print qx"faToNib $_ $dir/$name.nib"'
cd ..
```
Configure and run the pipeline
------------------------------
```
export PERL5LIB=${PERL5LIB}:src
init_pipeline.pl src/OxfordPlots.pm --pipeline_url sqlite:///oxford_plot --ref_genome homo_sapiens
beekeeper.pl --url sqlite:///oxford_plot --loop
```
File organisation
=================
(INPUT_DIR after downloading the sequences)
genomes
genomes/homo_sapiens
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa
genomes/pan_troglodytes
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa
(INPUT_DIR after calculating the sequence lengths)
genomes
genomes/homo_sapiens
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa
genomes/homo_sapiens.txt
genomes/pan_troglodytes
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa
genomes/pan_troglodytes.txt
(INPUT_DIR after running faToNib)
genomes
genomes/homo_sapiens
genomes/homo_sapiens/1.nib
genomes/homo_sapiens/2.nib
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa
genomes/homo_sapiens/Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa
genomes/homo_sapiens.txt
genomes/pan_troglodytes
genomes/pan_troglodytes/1.nib
genomes/pan_troglodytes/2A.nib
genomes/pan_troglodytes/2B.nib
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa
genomes/pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa
genomes/pan_troglodytes.txt
(OUTPUT_DIR after running the pipeline)
alignments/
alignments//pan_troglodytes
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.1.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2A.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.1.fa.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.axt
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.chain.rdotplot
alignments//pan_troglodytes/Pan_troglodytes.CHIMP2.1.4.dna_sm.chromosome.2B.fa.vs.Homo_sapiens.GRCh38.dna_sm.chromosome.2.fa.rdotplot
alignments//Pan_troglodytes.pdf