add: more comments
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2 changed files with 13 additions and 0 deletions
10
RGBEPP.sh
10
RGBEPP.sh
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@ -303,6 +303,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
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check_var "ARG_L"
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check_path "PathSortdiamond"
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# extract fasta file from diamond balst style output
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for (( i=0; i<$length_fn; i++ )); do
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$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
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done
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@ -316,9 +317,12 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
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check_var "ARG_L"
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check_path "PathSplitfasta"
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# split fasta into different folders based on sequence names
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for (( i=0; i<$length_fn; i++ )); do
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$PathSplitfsata ${full_names[$i]}.fasta
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done
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# mv to destdir
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find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
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cd -
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fi
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@ -330,13 +334,18 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
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mkdir -p $DirMerge
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cd $DirSplit
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# merge different taxa sequences in same gene to one fasta
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for (( i=0; i<$length_gn; i++ ))
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do
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cd ${genes[$i]}
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cat * > ../${genes[$i]}.fasta
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cd ..
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done
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# mv to destdir
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mv *.fasta ../$DirMerge
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cd -
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fi
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@ -354,6 +363,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
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mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
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cd $DirMerge
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# align the sequence based on codon
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parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
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cd -
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@ -80,7 +80,9 @@ void readInputFile(const string &filename,
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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// subject seq id
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string key = fields[1];
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// bit score
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double value = stod(fields[11]);
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// Check if the key already exists in the map
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if (max_map.find(key) != max_map.end()) {
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@ -106,6 +108,7 @@ void processMap(const map<string, pair<double, string>> &max_map,
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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// check if qstart is larger than qend
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if (stoi(fields[6]) > stoi(fields[7])) {
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fields[17] = revcomp(fields[17]);
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}
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