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Add sort_peptides back temporarily #51

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Add sort_peptides back temporarily #51

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18 changes: 16 additions & 2 deletions scripts/build_database.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -661,6 +661,17 @@ calculate_original_fas() {
}


sort_peptides() {
have "$INTDIR/peptides_by_original.tsv.lz4" || return
log "Started sorting the peptides table."
mkdir -p "$OUTPUT_DIR"
$CMD_LZ4CAT "$INTDIR/peptides_by_original.tsv.lz4" \
| LC_ALL=C $CMD_SORT -n \
| $CMD_LZ4 - > "$OUTPUT_DIR/peptides.tsv.lz4"
log "Finished sorting the peptides table."
}


create_sequence_table() {
have "$INTDIR/LCAs_original.tsv.lz4" "$INTDIR/LCAs_equalized.tsv.lz4" "$INTDIR/FAs_original.tsv.lz4" "$INTDIR/FAs_equalized.tsv.lz4" "$INTDIR/sequences.tsv.lz4" || return
log "Started the creation of the sequences table."
Expand Down Expand Up @@ -802,6 +813,8 @@ database)
wait $pid2
wait $pid3
wait $pid4
reportProgress "-1" "Sorting peptides." 8 # TODO remove this step for Postgres
sort_peptides
reportProgress "-1" "Creating sequence table." 9
create_sequence_table
rm "$INTDIR/LCAs_original.tsv.lz4"
Expand All @@ -810,8 +823,9 @@ database)
rm "$INTDIR/FAs_equalized.tsv.lz4"
rm "$INTDIR/sequences.tsv.lz4"
rm "$INTDIR/peptides_by_equalized.tsv.lz4"
# Use the original sort as the result
mv "$INTDIR/peptides_by_original.tsv.lz4" "$OUTPUT_DIR/peptides.tsv.lz4"
# Use the original sort as the result TODO this does not play nicely for MariaDB
# mv "$INTDIR/peptides_by_original.tsv.lz4" "$OUTPUT_DIR/peptides.tsv.lz4"
rm "$INTDIR/peptides_by_original.tsv.lz4"
reportProgress "-1" "Fetching EC numbers." 10
fetch_ec_numbers
reportProgress "-1" "Fetching GO terms." 11
Expand Down
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