From aaea0bcf7a4af5ad3358594d5e71e622381eaa2e Mon Sep 17 00:00:00 2001
From: Acribbs <a.p.cribbs@gmail.com>
Date: Mon, 1 Apr 2024 15:58:10 +0100
Subject: [PATCH] removed transfac script as its better placed in a pipeline

---
 cgat/tools/transfac2transfac.py   | 130 ------------------------------
 doc/scripts/transfac2transfac.rst |   5 --
 2 files changed, 135 deletions(-)
 delete mode 100644 cgat/tools/transfac2transfac.py
 delete mode 100644 doc/scripts/transfac2transfac.rst

diff --git a/cgat/tools/transfac2transfac.py b/cgat/tools/transfac2transfac.py
deleted file mode 100644
index e7859526..00000000
--- a/cgat/tools/transfac2transfac.py
+++ /dev/null
@@ -1,130 +0,0 @@
-'''
-transfac2transfac.py - filter transfac motif files
-====================================================
-
-:Tags: Python
-
-Purpose
--------
-
-Filter a transfac motif file.
-
-Usage
------
-
-Example::
-
-   python cgat_script_template.py
-
-Type::
-
-   python cgat_script_template.py --help
-
-for command line help.
-
-Command line options
---------------------
-
-'''
-
-
-import sys
-import re
-import cgatcore.experiment as E
-
-
-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__)
-
-    parser.add_argument("--version", action='version', version="1.0")
-
-    parser.add_argument(
-        "-f", "--filter-prefix", dest="filter_prefix", default=None,
-        help="ID prefix to filter on, eg. V for vertebrates")
-
-    parser.add_argument(
-        "-p", "--pattern-identifier", dest="filter_pattern", default=None,
-        help="ID pattern to filter (filter is case insensitive) eg. pax6. "
-        "Multiple patterns should be specified as a comma separated list")
-
-    (args) = E.start(parser)
-
-    if args.filter_pattern:
-        patterns = [x.strip() for x in args.filter_pattern.split(",")]
-        E.info("Supplied patterns %s" % ", ".join(patterns))
-    else:
-        patterns = False
-
-    filtered_motifs = []
-    n = 0
-
-    inmotif, tid, filter_emit, pattern_emit = False, False, False, False
-
-    for line in args.stdin:
-
-        # pick up motif start and ends.
-        if line.startswith("AC") and inmotif is False:
-            # print "in align"
-            inmotif = True
-            motif = line
-            continue
-        elif line.startswith("ID") and inmotif is True:
-            # print line
-            tid = line.split("  ")[1]
-            motif += line
-            continue
-
-        elif line.startswith("//") and inmotif is True:
-
-            motif += line
-
-            if tid is False:
-                raise ValueError("matrix ID not determined")
-
-            if args.filter_prefix:
-                if tid.startswith(args.filter_prefix):
-                    filter_emit = True
-            else:
-                filter_emit = True
-
-            if patterns is not False:
-                for pat in patterns:
-                    match = re.search(pat, tid, re.IGNORECASE)
-                    if match is not None:
-                        pattern_emit = True
-                        break
-            else:
-                pattern_emit = True
-
-            if filter_emit is True and pattern_emit is True:
-                filtered_motifs.append(motif)
-                n += 1
-
-            inmotif, tid, filter_emit, pattern_emit = (
-                False, False, False, False)
-            continue
-
-        elif inmotif is True:
-            motif += line
-
-        elif inmotif is False:
-            continue
-
-        else:
-            raise ValueError("unknown parsing state")
-
-    args.stdout.write("".join(filtered_motifs))
-
-    E.stop()
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv))
diff --git a/doc/scripts/transfac2transfac.rst b/doc/scripts/transfac2transfac.rst
deleted file mode 100644
index 33e0cf72..00000000
--- a/doc/scripts/transfac2transfac.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-
-.. automodule:: cgat.tools.transfac2transfac
-
-.. program-output:: cgat transfac2transfac -?
-