diff txtdiagnosis.py @ 1:b94872d65050 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/txtdiagnosis.py	Thu Jul 16 07:35:26 2020 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+import pandas as pd
+from argparse import ArgumentParser
+import sys
+
+
+def is_number(s):
+    try:
+        float(s)
+        return True
+    except ValueError:
+        return False
+
+
+def error_report(input_file, fname, output_file):
+    errors = 0
+    df = pd.read_table(input_file)
+    with open(output_file, "w") as outf:
+        for cols in df.columns.values:
+            if df[cols].count() != len(df[cols]):
+                with open(input_file, "r") as checkfile:
+                    fl = checkfile.readline()
+                    count_lines = 1
+                    for checklines in checkfile:
+                        to_check = checklines.strip().split("\t")
+                        count_lines += 1
+                        for item in to_check:
+                            if not is_number(item):
+                                errors += 1
+                                outf.write(" ".join(["WARNING: line", str(count_lines), "in", fname, "contains non-numeric results\n"]))
+        if errors == 0:
+            outf.write("No errors in the file.\n")
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="txtDiagnosis",
+             description="Reports potential errors in text-converted FCS files")
+
+    parser.add_argument(
+            '-i',
+            dest="input_file",
+            required=True,
+            help="File location for the text file.")
+
+    parser.add_argument(
+            '-n',
+            dest="filename",
+            required=True,
+            help="Filename location for the text file.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    args = parser.parse_args()
+
+    error_report(args.input_file, args.filename, args.output_file)