vg_annotate.sh

#!/bin/bash
# Goals:
# - Add bed annotation using odgi to try to display gene annotations in seqtubemap
# Contact: Colin Davenport

echo "Requires: odgi and vg toolsets"
echo "Usage: bash vg_annotate.sh input.og input_gff3 corrected_path"
echo "Usage: bash vg_annotate.sh input.og input_gff3 MA_genotype=chr9_133258121-134258121"

infile=$1
features=$2
corrected_path=$3
if [ -z $infile ];
        then
        echo "Specify input odgi as argument 1" && exit 1
else
        echo "Input file: $infile"
fi
if [ -z $features ];
        then
        echo "Specify input features as argument 2" && exit 1
else
        echo "Input file: $features"
fi
if [ -z $corrected_path ];
        then
        echo "Specify corrected_path as argument 3" && exit 1
else
        echo "Input path: $corrected_path"
fi

#paths to containers
#vg='singularity exec image.sif vg '
odgi='singularity exec image.sif odgi '

############
## odgi add annotation
###########

# Convert gene lines in the gff3 to bed, correcting coordinates. Can be more legible as an awk script. No gene annotation.
awk 'BEGIN {OFS = "\t";} $3 == "exon" {print $1, $4 - 1, $5, $9}' $features > genes.bed

# Correct path coords in the bed
awk -v path="$corrected_path" 'BEGIN {OFS = "\t";} {print path, $2, $3, $4}' genes.bed > genes_corrected.bed

echo "INFO: Reporting paths in odgi "
$odgi paths -L -i $infile

echo "INFO: Reporting 2 paths from each bed before and after modification - must match those in odgi to be displayed "
head -n 2 genes.bed
head -n 2 genes_corrected.bed


# inject the bed into the odgi
$odgi inject -b genes_corrected.bed -i $infile -o $infile.annot.og




## vg part - unused at present

############
## Convert, simplify, reconvert to odgi - uses vg old protobuf format, which vg simplify probably needs, 1 warning, no errors
###########

# Convert odgi to gfa
#odgi convert or view, is this needed? Is gfa or odgi standard interchange format

# Convert gfa to vg
#$vg convert -v -g $infile > $infile.vg

# Simplify - remove SNPs, indels below 10bp
#$vg simplify -t 4 -m 10 $infile.vg > $infile.nosnarls.vg

# now convert back to gfa -> then to odgi
#$vg convert -f $infile.nosnarls.vg > $infile.nosnarls.gfa
#$odgi build -g $infile.nosnarls.gfa -o $infile.nosnarls.og

These are just ideas which did work, I'm not very satisfied with it. I think vg and odgi annotation techniques need to improve a lot.