malacology/RGBEPP
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kuoi 2024-07-05 11:53:06 +10:00
parent 680c5392e6
commit df84006179
2 changed files with 13 additions and 0 deletions
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10
RGBEPP.sh
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@ -303,6 +303,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
check_var "ARG_L" check_var "ARG_L"
check_path "PathSortdiamond" check_path "PathSortdiamond"
# extract fasta file from diamond balst style output
for (( i=0; i<$length_fn; i++ )); do for (( i=0; i<$length_fn; i++ )); do
$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta $PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
done done
@ -316,9 +317,12 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
check_var "ARG_L" check_var "ARG_L"
check_path "PathSplitfasta" check_path "PathSplitfasta"
# split fasta into different folders based on sequence names
for (( i=0; i<$length_fn; i++ )); do for (( i=0; i<$length_fn; i++ )); do
$PathSplitfsata ${full_names[$i]}.fasta $PathSplitfsata ${full_names[$i]}.fasta
done done
# mv to destdir
find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \; find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
cd - cd -
fi fi
@ -330,13 +334,18 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
mkdir -p $DirMerge mkdir -p $DirMerge
cd $DirSplit cd $DirSplit
# merge different taxa sequences in same gene to one fasta
for (( i=0; i<$length_gn; i++ )) for (( i=0; i<$length_gn; i++ ))
do do
cd ${genes[$i]} cd ${genes[$i]}
cat * > ../${genes[$i]}.fasta cat * > ../${genes[$i]}.fasta
cd .. cd ..
done done
# mv to destdir
mv *.fasta ../$DirMerge mv *.fasta ../$DirMerge
cd - cd -
fi fi
@ -354,6 +363,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
cd $DirMerge cd $DirMerge
# align the sequence based on codon
parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}" parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
cd - cd -

3
sortdiamond.cpp
View file

@ -80,7 +80,9 @@ void readInputFile(const string &filename,
while (iss >> fields[i] && i < 20) { while (iss >> fields[i] && i < 20) {
i++; i++;
} }
// subject seq id
string key = fields[1]; string key = fields[1];
// bit score
double value = stod(fields[11]); double value = stod(fields[11]);
// Check if the key already exists in the map // Check if the key already exists in the map
if (max_map.find(key) != max_map.end()) { if (max_map.find(key) != max_map.end()) {
@ -106,6 +108,7 @@ void processMap(const map<string, pair<double, string>> &max_map,
while (iss >> fields[i] && i < 20) { while (iss >> fields[i] && i < 20) {
i++; i++;
} }
// check if qstart is larger than qend
if (stoi(fields[6]) > stoi(fields[7])) { if (stoi(fields[6]) > stoi(fields[7])) {
fields[17] = revcomp(fields[17]); fields[17] = revcomp(fields[17]);
} }