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pubchem/pubchem/descriptor/prefix_add.bash

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+#!/bin/bash
+
+# Directory to search for .ttl files.
+search_dir="."
+
+# File containing the prefix.
+prefix_file="prefix"
+
+# Check if the prefix file exists.
+if [[ ! -f "$prefix_file" ]]; then
+    echo "Error: '$prefix_file' not found."
+    exit 1
+fi
+
+# Find and process each .ttl file.
+find "$search_dir" -type f -name "*.ttl" -exec sh -c '
+    for ttl_file do
+        # Create temporary files.
+        temp_file=$(mktemp)
+        temp_file2=$(mktemp)
+
+        # Remove lines starting with @prefix and write to the temporary file.
+        grep -v '^@prefix' "$ttl_file" > "$temp_file2"
+
+        # Prepend the prefix to the .ttl file and write to the temporary file.
+        cat "$1" "$temp_file2" > "$temp_file"
+
+        # Move the temporary file to the original .ttl file.
+        mv "$temp_file" "$ttl_file"
+
+        # Remove the temporary files.
+        rm "$temp_file2"
+    done
+' _ "$prefix_file" {} +

pubchem/pubchem/descriptor/split_ttl_gz.bash

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+#! /bin/bash
+
+# splitlines is a variable that tells the script after how many 
+# Turtle triples groups it should split. At the moment, we simply 
+# split by assuming that each trailing '.' at the end of a line
+# ends a triples group.
+# The default is 200000000 but depending on the size of your 
+# ttl.gz or your memory you may want to decide for smaller chunks.
+# splitlines can be changed/overridden with option -l
+splitlines=1000000
+
+# auxchar is an auxiliary character 
+# that the script needs to replace end of lines 
+# in an intermediate step. you need to make sure
+# that it doesn't appear in the turtle file you want to split.
+# auxchar can be changed/overridden with option -x
+auxchar=±
+
+while getopts l:x: opt; do
+  case $opt in
+  l)
+  splitlines=$OPTARG
+  echo "splitlines set to $splitlines explicitly by option -l" >&2
+  ;;
+  x)
+  auxchar=$OPTARG
+  echo "auxchar set to $auxchar explicitly by option -x" >&2
+  ;;
+  \?)
+  echo "Invalid option: -$OPTARG" >&2
+  ;;
+  esac
+done
+
+#get the last argument (filename) expects a ttl.gz:
+fn="${@: -1}"
+
+# Then create all the split gz files:
+# Note: the last ${fn}.gz probably creates files named .gz.gz but who cares.
+
+splitfiles=(*_${fn}_split*)
+
+if [ -e "${splitfiles[0]}" ] || [ -e "prefixes_${fn}.gz" ]
+then
+  echo "splits or prefix file for file ${fn} already exist!"
+else
+  # First, extract a file containing all the prefixes...
+  echo "Creating prefixes_${fn}.gz"
+  gunzip -c ${fn} | grep @prefix |sort -u | gzip > prefixes_${fn}.gz
+  
+  # ... then, create the actual split files
+  echo "Creating split files"
+  zcat ${fn}| grep -v @prefix | sed -e s/'\.$'/"$auxchar"/g | \
+ tr '\n' ' ' | tr "$auxchar" '\n' | grep -v -e '^[ ]*$' | \
+ sed -e s/'$'/' .'/ | \
+ split -l$splitlines --additional-suffix=_${fn}_split --filter='gzip > $FILE.gz'
+fi

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