Add script to perform initial validation

Author: caduribas

training/validate-mrna-and-rna-seq-articles.py

@@ -0,0 +1,52 @@
+import csv
+
+
+def find_string(line, keywords):
+    """
+    Check if any of the keywords are present in the line.
+
+    Args:
+        line (iterable): An iterable containing items to be checked.
+        keywords (list of str): A list of keywords to search for in the line.
+
+    Returns:
+        bool: True if any keyword from the list is found in the line, False otherwise.
+    """
+    return any(keyword in str(item).lower() for keyword in keywords for item in line)
+
+
+def main():
+    """
+    Main function to process a CSV file and check for specific keywords in each line.
+    We need RNA-related and non-RNA-related articles that mention "mrna" or "rna-seq".
+    """
+    try:
+        with open("check_abstracts.csv", mode="r", encoding="utf-8") as file:
+            read_csv = csv.reader(file)
+            keyword = [
+                "non-coding", "noncoding", "ncrna", "rrna", "lncrna", "sncrna", "mirna", "trna", "rbp", "snrna", "pirna",
+                "lincrna", "scrna", "pre-mirna", "riboswitch"
+            ]
+
+            for line_number, line in enumerate(read_csv, start=1):
+                if line_number == 1:
+                    continue
+                elif 2 <= line_number <= 101:
+                    if not find_string(line, ["mrna"]):
+                        print(f"Line {line_number} does not contain 'mrna': {line}")
+                elif 102 <= line_number <= 201:
+                    if not find_string(line, ["mrna"]) or find_string(line, keyword):
+                        print(f"Please check line {line_number}: {line}")
+                elif 202 <= line_number <= 301:
+                    if not find_string(line, ["rna-seq"]):
+                        print(f"Line {line_number} does not contain 'rna-seq': {line}")
+                else:
+                    if not find_string(line, ["rna-seq"]) or find_string(line, keyword):
+                        print(f"Please check line {line_number}: {line}")
+
+    except Exception as e:
+        print(f"Oops! We've had a problem: {e}")
+
+
+if __name__ == "__main__":
+    main()