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|
#!/bin/bash
usage="\
Usage:
$(basename "$0") -P stacks_dir -B bam_file [-q min_MAPQ=20] -O out_dir
Extracts the coordinates of the RAD loci from the given BAM file into a
'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and
'catalog.calls' files so that they include the genomic coordinates given in the
input BAM file.
"
version="_VERSION_"
# Check dependencies
# ==========
command -v python3 &>/dev/null || { python3; echo "Error: Python 3 is required." >&2; exit 1; }
command -v samtools &>/dev/null || { samtools; echo "Error: Samtools is required." >&2; exit 1; }
# Parse arguments
# ==========
# If there aren't any arguments, print the help.
[[ $# -gt 0 ]] || { echo -n "$usage"; exit 1; }
# Check that there aren't weird characters in the input.
for arg in "$@" ;do
if [[ "$arg" =~ [^[:alnum:]_.,/~+=:-] ]] ;then
echo "Error: illegal character in argument '$arg'." >&2
exit 1
fi
done
# Parse arguments.
min_mapq=20
while getopts 'P:B:O:q:hv' opt ;do
case "$opt" in
P) stacks_d="${OPTARG/%\//}" ;;
B) bam_f="${OPTARG/%\//}" ;;
O) out_d="${OPTARG/%\//}" ;;
q) min_mapq="$OPTARG" ;;
h) echo -n "$usage" >&2; exit 1 ;;
v) echo "$version" >&2; exit 1 ;;
*) echo "Error: Bad arguments (-h for help)." >&2; exit 1 ;;
esac
done
shift $((OPTIND-1))
if [[ $# -ne 0 ]] ;then
echo "Error: '$1' is seen as a positional argument (expected no positional arguments)." >&2
exit 1
fi
# Check them.
[[ "$stacks_d" ]] || { echo "Error: -P is required." >&2; exit 1; }
[[ "$bam_f" ]] || { echo "Error: -B is required." >&2; exit 1; }
[[ "$out_d" ]] || { echo "Error: -O is required." >&2; exit 1; }
[[ "$min_mapq" =~ ^[0-9]+$ ]] || { echo "Error: -q expects a positive integer (received '$min_mapq')." >&2; exit 1; }
[[ -e "$stacks_d" ]] || { ls -- "$stacks_d"; exit 1; }
[[ -e "$bam_f" ]] || { ls -- "$bam_f"; exit 1; }
fa="$stacks_d/catalog.fa.gz"
vcf="$stacks_d/catalog.calls"
[[ -e "$fa" ]] || { ls -- "$fa"; exit 1; }
[[ -e "$vcf" ]] || { ls -- "$vcf"; exit 1; }
o_coords="$out_d/locus_coordinates.tsv"
o_fa="$out_d/catalog.fa.gz"
o_vcf="$out_d/catalog.calls"
[[ ! -e "$o_coords" ]] || { echo "Error: Refusing to overwrite '$o_coords'." >&2; exit 1; }
[[ ! -e "$o_fa" ]] || { echo "Error: Refusing to overwrite '$o_fa'." >&2; exit 1; }
[[ ! -e "$o_vcf" ]] || { echo "Error: Refusing to overwrite '$o_vcf'." >&2; exit 1; }
# If something goes wrong, stop & print an error.
set -e -o pipefail
trap "echo 'Error: aborted.' >&2" EXIT
# Make sure we have write permissions.
mkdir -p "$out_d"
touch "$o_fa" "$o_vcf"
# Retrieve the highest ID in the catalog.
# ==========
echo "Finding the highest current locus ID..."
id=$(gzip -cd "$fa" | tail -n2 | head -n1 | awk '{print $1}')
if [[ ! "$id" =~ ^\>[0-9]+$ ]] ;then
echo "Error: Unexpected format in '$fa'; the second to last line was:" >&2
gzip -cd "$fa" | tail -n2 | head -n1
exit 1
fi
id=$(echo "$id" | cut -c2-)
echo "$id"
echo
# Write the old_id : new_id : pos file.
# ==========
echo "Extracting locus coordinates..."
samtools view -F 0x904 -q "$min_mapq" "$bam_f" |
# Convert SAM to `LOCUS_ID \t CHR \t POS \t STRAND`.
awk -F '\t' -v OFS='\t' '{
if (int( $2 % (2*16) / 16 )) {
# Negative strand.
pos = $4 - 1
gsub(/[0-9]+[ISH]/, "", $6)
gsub(/[A-Z]/, ",", $6)
n = split(substr($6, 1, length($6)-1), cig, ",")
for (i=1; i<=n; ++i) { pos += cig[i] }
print $1, $3, pos, "-"
} else {
print $1, $3, $4, "+"
}
}' |
# Sort by chromosome.
sort -k2,2 |
# Pull the reference chromosome order from the BAM header.
join -t $'\t' -12 -22 -o "1.1 1.2 2.1 1.3 1.4" \
- \
<(samtools view -H "$bam_f" |
grep '^@SQ' | grep -oE $'SN:[^\t]+' | cut -c4- |
awk '{printf NR"\t"$1"\n"}' |
sort -k2,2
) |
# Sort by chromosome index, bp & strand, then remove the index.
sort -k3,3n -k4,4n -k5,5r | cut -f 1,2,4,5 |
# Create the new IDs (we start at the power of 10 above the current max).
awk 'BEGIN{id = '"$id"' + 1} {printf id++ "\t" $1 "\t" $2 ":" $3 ":" $4 "\n"}' |
# Add a header.
{ echo -e 'id_new\tid_old\taln_pos'; cat; } \
> "$o_coords"
[[ $(wc -l < "$o_coords") -gt 1 ]] || { echo "Error: Extraction of coordinates failed; check BAM file." >&2; exit 1; }
echo "Wrote '$o_coords'."
echo
# Write the new FASTA file.
# ==========
echo "Rewriting locus sequences and information..."
gzip -cd "$fa" |
tr -d '\r' | paste -d '\r' - - | sed 's/^>//' |
awk -F' ' -v OFS=' ' '
BEGIN{
while(getline < "'"$o_coords"'") {
if (! /^id_new/) {
old2new[$2] = $1
old2pos[$2] = $3
}
}
} {
old_id = $1
if (old_id in old2new) {
$1 = old2new[old_id] " pos=" old2pos[old_id]
print
}
}' |
sort -k1,1n |
sed 's/^/>/' | tr '\r' '\n' |
gzip \
> "$o_fa"
echo "Wrote '$o_fa'."
echo
# Write the new VCF file.
# ==========
echo "Rewriting variants..."
{
# Copy the header.
{ gzip -cd "$vcf" 2>/dev/null || true; } | sed '/^#CHROM/ q' # (gzip unhappy about the closed pipe).
# Update & resort the records.
gzip -cd "$vcf" | grep -v '^#' |
awk -F'\t' -v OFS='\t' '
BEGIN{
while(getline < "'"$o_coords"'") {
if (! /^id_new/) {
old2new[$2] = $1
}
}
} {
old_id = $1
if (old_id in old2new) {
$1 = old2new[old_id]
print
}
}' |
sort -k1,1n -k2,2n
} | gzip \
> "$o_vcf"
echo "Wrote '$o_vcf'."
echo
trap - EXIT
echo "$(basename "$0") is done."
|
