diff --git a/cgat/tools/cgat_fasta2cDNA.py b/cgat/tools/cgat_fasta2cDNA.py
deleted file mode 100644
index 6305f2de..00000000
--- a/cgat/tools/cgat_fasta2cDNA.py
+++ /dev/null
@@ -1,76 +0,0 @@
-'''
-cgat_fasta2cDNA.py - converting multi-fasta of exon features into a multi-fasta of spliced cDNAs/RNAs
-======================================================================================================
-
-:Tags: Python
-
-Purpose
--------
-
-Usage
------
-
-.. Example use case
-
-Example::
-
-   python cgat_fasta2cDNA.py
-
-Type::
-
-   python cgat_fasta2cDNA.py --help
-
-for command line help.
-
-Command line options
---------------------
-
-'''
-
-import sys
-import cgatcore.experiment as E
-import cgatcore.iotools as iotools
-
-
-def makeSplicedFasta(infile):
-    '''
-    Merge fasta sequences together into a single
-    spliced transcript sequence
-    '''
-
-    fasta_dict = {}
-    with iotools.open_file(infile) as fafile:
-        for line in fafile.readlines():
-            if line[0] == '>':
-                header = line.rstrip("\n")
-                fasta_dict[header] = ''
-            else:
-                fasta_dict[header] += line.rstrip("\n")
-
-    for key, value in sorted(fasta_dict.items()):
-        yield "%s\n%s\n" % (key, value)
-
-
-def main(argv=None):
-    """script main.
-    parses command line options in sys.argv, unless *argv* is given.
-    """
-
-    if argv is None:
-        argv = sys.argv
-
-    # setup command line parser
-    parser = E.ArgumentParser(description=__doc__)
-
-    # add common options (-h/--help, ...) and parse command line
-    (args) = E.start(parser, argv=argv)
-
-    infile = argv[-1]
-    for record in makeSplicedFasta(infile):
-        options.stdout.write(record)
-
-    # write footer and output benchmark information.
-    E.stop()
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))