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Merge pull request #246 from waveygang/forcably-biwfa
optionally force global biwfa alignment of mappings
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Original file line number | Diff line number | Diff line change |
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#!/bin/bash | ||
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# Function to display usage | ||
usage() { | ||
echo "Usage: $0 -p <paf_file> -f <fasta_file> -o <output_prefix>" | ||
echo " -p, --paf PAF file" | ||
echo " -f, --fasta FASTA file" | ||
echo " -o, --output Output prefix for the new FASTA and adjusted PAF files" | ||
exit 1 | ||
} | ||
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# Parse command-line arguments | ||
PARSED_ARGUMENTS=$(getopt -a -n "$0" -o p:f:o: --long paf:,fasta:,output: -- "$@") | ||
VALID_ARGUMENTS=$? | ||
if [ "$VALID_ARGUMENTS" != "0" ]; then | ||
usage | ||
fi | ||
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eval set -- "$PARSED_ARGUMENTS" | ||
while : | ||
do | ||
case "$1" in | ||
-p | --paf) PAF_FILE="$2" ; shift 2 ;; | ||
-f | --fasta) FASTA_FILE="$2" ; shift 2 ;; | ||
-o | --output) OUTPUT_PREFIX="$2" ; shift 2 ;; | ||
--) shift ; break ;; | ||
*) usage ;; | ||
esac | ||
done | ||
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# Validate arguments | ||
if [ -z "$PAF_FILE" ] || [ -z "$FASTA_FILE" ] || [ -z "$OUTPUT_PREFIX" ]; then | ||
usage | ||
fi | ||
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OUTPUT_FASTA="${OUTPUT_PREFIX}.fa" | ||
OUTPUT_PAF="${OUTPUT_PREFIX}.paf" | ||
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# Extract the first alignment from the PAF file | ||
read -r line < "$PAF_FILE" | ||
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# Parse the alignment fields | ||
IFS=$'\t' read -r -a fields <<< "$line" | ||
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# Extract query and target information | ||
query_name="${fields[0]}" | ||
query_start="${fields[2]}" | ||
query_end="${fields[3]}" | ||
target_name="${fields[5]}" | ||
target_start="${fields[7]}" | ||
target_end="${fields[8]}" | ||
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# Extract sequences using samtools faidx | ||
samtools faidx "$FASTA_FILE" "$query_name:$query_start-$query_end" > "$OUTPUT_FASTA" | ||
samtools faidx "$FASTA_FILE" "$target_name:$target_start-$target_end" >> "$OUTPUT_FASTA" | ||
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qname=$(grep ^">" "$OUTPUT_FASTA" | head -n 1 | sed 's/^>//') | ||
tname=$(grep ^">" "$OUTPUT_FASTA" | tail -n 1 | sed 's/^>//') | ||
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# Adjust the PAF file | ||
awk -v qname=$qname \ | ||
-v tname=$tname \ | ||
'{ | ||
if (NF > 0) { | ||
query_length = $4 - $3; | ||
target_length = $9 - $8; | ||
$1 = qname; | ||
$6 = tname; | ||
$2 = query_length; | ||
$3 = 0; | ||
$4 = query_length; | ||
$7 = target_length; | ||
$8 = 0; | ||
$9 = target_length; | ||
print $0; | ||
} | ||
}' "$PAF_FILE" | tr ' ' '\t' > "$OUTPUT_PAF" | ||
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