diff name_changer.py @ 0:58ad7b512590 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/name_changer.py	Thu May 12 09:48:15 2016 -0400
@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+
+import optparse
+import os.path
+
+
+def fix_header_line(start_header, header_line, new_names):
+    header_parts = header_line.split("\t")
+    if len(header_parts) <= len(start_header):
+        raise Exception("Only found {0} columns in second (header) line expected at least {1}.".format(len(header_parts), (len(start_header) + 1)))
+    data_headers = header_parts[:len(start_header)]
+    if data_headers != start_header:
+        raise Exception("Unexpected start to second (header) line Found: ")
+    new_header = "\t".join(start_header)
+    file_headers = header_parts[len(start_header):]
+    if len(file_headers) != len(new_names):
+        raise Exception("Found {0} file columns in header line, but {1} new_name paramters provided.".format(len(file_headers), len(new_names)))
+    for i in range(len(file_headers)):
+        new_header += "\t"
+        new_header += new_names[i]
+    new_header += "\n"
+    return new_header
+
+
+def clean_names(prefix, old_names):
+    if len(old_names) > 1:
+        shared_start = old_names[0].strip()
+        shared_ends = old_names[0].strip()
+        for name in old_names:
+            clean = name.strip()
+            while len(shared_start) > 0 and (not clean.startswith(shared_start)):
+                shared_start = shared_start[:-1]
+            while len(shared_ends) > 0 and (not clean.endswith(shared_ends)):
+                shared_ends = shared_ends[1:]
+        start = len(shared_start)
+        end = 0 - len(shared_ends)
+    else:
+        start = 0
+        end = 0
+    new_names = []
+    if end < 0:
+        for name in old_names:
+            new_names.append(prefix + name.strip()[start:end])
+    else:
+        for name in old_names:
+            new_names.append(prefix + name.strip()[start:])
+    return new_names
+
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option("--raw_count_file", action="store", type="string", default=None, help="path to file original with the counts")
+    parser.add_option("--fixed_count_file", action="store", type="string", default=None, help="new path for renamaned counts file")
+    parser.add_option("--raw_summary_file", action="store", type="string", default=None, help="path to file original with the summary")
+    parser.add_option("--fixed_summary_file", action="store", type="string", default=None, help="new path for renamaned summary file")
+    parser.add_option("--names_file", action="store", type="string", default=None, help="path to file which contains the names.")
+    parser.add_option("--new_name", action="append", type="string", default=None,
+                      help="Names to be used. Must be the same length as in the raw_count_file")
+    parser.add_option("--names_prefix", action="store", type="string", default="", help="Prefix to add in from of every name.")
+
+    (options, args) = parser.parse_args()
+
+    if not os.path.exists(options.raw_count_file):
+        parser.error("Unable to find raw_count_file {0}.".format(options.raw_count_file))
+    if options.names_file:
+        if options.new_name:
+            parser.error("names_file parameter clashes with new_names paramter(s)")
+        if not os.path.exists(options.names_file):
+            parser.error("Unable to find names_file {0}.".format(options.names_file))
+        new_names = []
+        with open(options.names_file, "r") as names_file:
+            for line in names_file:
+                new_names.append(line.strip())
+        new_names = clean_names(options.names_prefix, new_names)
+    else:
+        if not options.new_name:
+            parser.error("No names_file or new_name paraters provided.")
+        new_names = options.new_name
+
+    print "Changing column names to ", new_names
+
+    with open(options.raw_count_file, "r") as input_file:
+        with open(options.fixed_count_file, "w") as output_file:
+            input_file.readline()  # job line
+            start_header = ["Geneid", "Chr", "Start", "End", "Strand", "Length"]
+            header_line = fix_header_line(start_header, input_file.readline(), new_names)
+            output_file.write(header_line)
+            for line in input_file:
+                output_file.write(line)
+
+    with open(options.raw_summary_file, "r") as input_file:
+        with open(options.fixed_summary_file, "w") as output_file:
+            start_header = ["Status"]
+            header_line = fix_header_line(start_header, input_file.readline(), new_names)
+            output_file.write(header_line)
+            for line in input_file:
+                output_file.write(line)
+
+
+if __name__ == "__main__":
+    main()