Helper bed.sh

src/seqtk/src/_helpers/bed.sh

@@ -0,0 +1,80 @@
+#!/bin/bash
+
+# Function to check if a file is a valid BED file
+check_bed_file() {
+    local file="$1"
+    num_columns=$(head -n 1 "$file" | cut -f 1- | tr '\t' '\n' | wc -l)
+
+    # Check if the file exists
+    if [[ ! -f "$file" ]]; then
+        echo "Error: The specified file does not exist."
+        return 1
+    fi
+
+    # Check if the file is non-empty
+    if [[ ! -s "$file" ]]; then
+        echo "Error: The specified file is empty."
+        return 1
+    fi
+
+    # Check if the file is a valid BED file (minimum 3 tab-separated columns)
+    if [[ $num_columns -lt 3 ]]; then
+        echo "The specified file is not a valid BED file. It should have at least three tab-separated columns."
+        return 1
+    fi
+
+    # Additional check: Ensure that the 6th column (if present) is either + or -
+    if [[ $num_columns -eq 6 ]]; then
+        while IFS=$'\t' read -r -a columns; do
+            columns[5]=${columns[5]%$'\n'}
+            if [[ ${columns[5]} == "+" || ${columns[5]} == "-" ]]; then
+                return 0
+            else 
+                echo "Error: The 6th column of the specified BED file should be either + or -."
+                #echo "Offending line: ${columns[5]}"
+                return 1
+            fi
+        done < "$file"
+    fi
+
+    return 0
+}
+
+# Function to check if a file is a valid list of FASTA file IDs
+check_fasta_id_list() {
+    local file="$1"
+
+    # Check if the file exists
+    if [[ ! -f "$file" ]]; then
+        echo "Error: The specified file does not exist."
+        return 1
+    fi
+
+    # Check if the file is non-empty
+    if [[ ! -s "$file" ]]; then
+        echo "Error: The specified file is empty."
+        return 1
+    fi
+
+    # Additional check: Ensure that each line contains only one word (FASTA ID)
+    if ! awk 'NF != 1 { exit 1 }' "$file"; then
+        return 1
+    fi
+
+    return 0
+}
+
+# Arguments:
+list_file="$1"
+
+# Check if the par_name_list is given and validate accordingly
+if [[ -n "$list_file" ]]; then
+    if check_fasta_id_list "$list_file"; then
+        echo "The specified file is a valid list of FASTA IDs."
+    elif check_bed_file "$list_file"; then
+        echo "The specified file is a valid BED file."
+    else
+        echo "Error: The specified file is neither a valid BED file nor a valid list of FASTA IDs."
+        exit 1
+    fi
+fi