Update existing gentrap scripts to the new namespace

biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/scripts/hist2count.py

+#!/usr/bin/env python
+"""
+Convert a histogram generated by coverageBed to counts per region.
+
+
+A histogram file can be generated with the following command:
+coverageBed -split -hist -abam sample.bam -b selection.bed > selection.hist
+
+The output consists of four columns:
+- Chromosome name.
+- Start position.
+- End position.
+- Number of nucleotides mapped to this region.
+- Normalised expression for this region.
+
+If the -c option is used, additional columns can be added.
+"""
+
+import argparse
+import sys
+
+def hist2count(inputHandle, outputHandle, copy):
+    """
+    Split a fasta file on length.
+
+    @arg inputHandle: Open readable handle to a histogram file.
+    @type inputHandle: stream
+    @arg outputHandle: Open writable handle to the counts file.
+    @type outputHandle: stream
+    @arg outputHandle: List of columns to copy to the output file.
+    @type outputHandle: list[int]
+    """
+    def __copy():
+        copyList = ""
+        for i in copy:
+            copyList += "\t%s" % data[i]
+        return copyList
+    #__copy
+
+    def __write():
+        outputHandle.write("%s\t%i\t%i\t%i\t%f%s\n" % (chromosome, start,
+                        end, count, float(count) / (end - start), copyList))
+
+    chromosome = ""
+    start = 0
+    end = 0
+    count = 0
+
+    for line in inputHandle.readlines():
+        data = line.split()
+
+        if not data[0] == "all":
+            start_temp = int(data[1])
+            end_temp = int(data[2])
+
+            if data[0] != chromosome or start_temp != start or end_temp != end:
+                if chromosome:
+                    __write()
+                chromosome = data[0]
+                start = start_temp
+                end = end_temp
+                count = 0
+                copyList = __copy()
+            #if
+            count += int(data[-4]) * int(data[-3])
+        #if
+    #for
+    __write()
+#hist2count
+
+def main():
+    """
+    Main entry point.
+    """
+    usage = __doc__.split("\n\n\n")
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=usage[0], epilog=usage[1])
+    parser.add_argument("-i", dest="input", type=argparse.FileType("r"),
+        default=sys.stdin, help="histogram input file (default=<stdin>)")
+    parser.add_argument("-o", dest="output", type=argparse.FileType("w"), 
+        default=sys.stdout, help="file used as output (default=<stdout>)")
+    parser.add_argument("-c", dest="copy", type=int, nargs="+", default=[],
+        help="copy a column to the output file")
+    args = parser.parse_args()
+
+    hist2count(args.input, args.output, args.copy)
+#main
+
+if __name__ == '__main__':
+    main()