diff getHeaders.py @ 1:05440ef97f8b draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getHeaders.py	Tue Jul 14 09:46:31 2020 -0400
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Version 1.2 - May 2018
+# added leeway for files with different nb of headers
+#
+
+
+import sys
+
+from argparse import ArgumentParser
+
+
+def print_headers(files, filenames, outfile):
+    header_table = {}
+    for i, eachfile in enumerate(files):
+        with open(eachfile, "r") as ef:
+            headers = ef.readline().strip()
+            header_table[filenames[i]] = headers.split("\t")
+
+    h = 0
+    for f in header_table:
+        j = len(header_table[f]) + 1
+        if j > h:
+            h = j
+
+    idx = [str(x) for x in range(1, h)]
+
+    with open(outfile, "w") as outf:
+        outf.write("Index\t")
+        outf.write("\t".join(idx) + "\n")
+        for f in header_table:
+            if len(header_table[f]) < h:
+                for k in range(len(header_table[f]), h-1):
+                    header_table[f].append("")
+                sys.stderr.write(str(len(header_table[f])))
+            outf.write(f + "\t")
+            outf.write("\t".join(header_table[f]) + "\n")
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="GetHeaders",
+             description="Gets the headers of all files in given set.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_files",
+            required=True,
+            action='append',
+            help="File location for the text files.")
+
+    parser.add_argument(
+            '-n',
+            dest="file_names",
+            required=True,
+            action='append',
+            help="File names.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    args = parser.parse_args()
+    input_files = [f for f in args.input_files]
+    file_names = [fn for fn in args.file_names]
+    print_headers(input_files, file_names, args.output_file)