diff replace_chromosome_names.py @ 0:97c11d04cd4c draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ commit 588282bf5cbb9909ad9cd8c316ec33158c858727

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/replace_chromosome_names.py	Thu May 18 14:17:48 2017 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import sys
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Replace chromosome names in a tabular (e.g. VCF) file using a mapping table.')
+    parser.add_argument('--cols', required=True, help='comma-separated list of column indexes (starting from 1) on which to perform the replacement')
+    parser.add_argument('-m', dest='mapping_file', type=argparse.FileType(), required=True, help='mapping table file. Must contain 2 tab-separated columns')
+    parser.add_argument('--comment-char', help='lines starting with this character will be directly printed to the output file')
+    parser.add_argument('-o', dest='output', type=argparse.FileType('w'), default=sys.stdout, help='output file. If not specified, writes on standard output')
+    parser.add_argument('input', metavar='INPUT', type=argparse.FileType(), help='tabular input file')
+    args = parser.parse_args()
+
+    map_dict = dict()
+    for line in args.mapping_file:
+        line = line.rstrip('\r\n')
+        line_cols = line.split('\t')
+        if len(line_cols) < 2:
+            raise Exception("Line '%s' in mapping table file does not contain 2 tab-separated columns" % line)
+        map_dict[line_cols[0]] = line_cols[1]
+
+    cols_to_map = [int(_) - 1 for _ in args.cols.split(',')]
+
+    for line in args.input:
+        line = line.rstrip('\r\n')
+        if args.comment_char and line.startswith(args.comment_char):
+            print(line, file=args.output)
+        else:
+            line_cols = line.split('\t')
+            for col_to_map in cols_to_map:
+                old_value = line_cols[col_to_map]
+                line_cols[col_to_map] = map_dict.get(old_value, old_value)
+            mapped_line = '\t'.join(line_cols)
+            print(mapped_line, file=args.output)
+
+
+if __name__ == "__main__":
+    main()