Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 02 Mar 2017 11:51:33 +0100
Description: Upstream tarball is lacking documented script.  This was
 fetched from Git and injected via quilt patch

--- /dev/null
+++ b/grepseq
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+from optparse import OptionParser
+import biotools.IO as io
+import re
+
+
+def search(regex, filename, options):
+    pfn = options.print_filename
+    snm = options.search_name
+    ssq = options.search_seq
+    inv = options.invert_results
+    cnt = options.count
+    cmx = options.max_count
+
+    if pfn and not cnt:
+        print '\n=======>', filename, '<=======\n'
+
+    for seq in io.open(filename, 'r'):
+        in_name = snm and regex.search(seq.name + ' ' + seq.defline)
+        in_seq = ssq and regex.search(seq.seq)
+        if not inv and (in_name or in_seq):
+            options.curr_count += 1
+            if not cnt:
+                print seq
+        elif inv and not (in_name or in_seq):
+            options.curr_count += 1
+            if not cnt:
+                print seq
+        if cmx and options.curr_count > cmx:
+            break
+
+    if cnt:
+        print options.curr_count
+
+if __name__ == '__main__':
+    optp = OptionParser(usage="%prog [options] <pattern> <files ...>")
+    optp.add_option('-c', '--count',
+                    action='store_true', dest='count', default=False,
+                    help='''Suppress normal output; instead print a count of
+                         matching lines for each input file. With the -v,
+                         --invert-match option (see below), count non-matching
+                         lines.''')
+    optp.add_option('-H', '--with-filename',
+                    action='store_true', dest='print_filename', default=False,
+                    help='Print the filename for each match.')
+    optp.add_option('-i', '--ignore-case',
+                    action='store_true', dest='ignore_case', default=False,
+                    help='''Ignore case distinctions in both the pattern and
+                         input files.''')
+    optp.add_option('-m', '--max-count', metavar='NUM',
+                    action='store', dest='max_count', default=None, type='int',
+                    help='''Stop reading a file after NUM matching lines. When
+                         the -c or --count option is also used, grepseq does
+                         not output a count greater than NUM. When the -v or
+                         --invert-match option is also used, grep stops after
+                         outputting NUM non-matching lines.''')
+    optp.add_option('-N', '--names-only',
+                    action='store_false', dest='search_seq', default=True,
+                    help='Search only sequence names. Cannot be used with -S.')
+    optp.add_option('-S', '--sequences-only',
+                    action='store_false', dest='search_name', default=True,
+                    help='Search only sequences. Cannot be used with -N.')
+    optp.add_option('-v', '--invert-match',
+                    action='store_true', dest='invert_results', default=False,
+                    help='''Invert the sense of matching, to select non-matching
+                         lines.''')
+
+    opts, args = optp.parse_args()
+    if len(args) < 2:
+        optp.print_help()
+        exit(1)
+
+    if opts.max_count is not None and opts.max_count < 1:
+        exit(0)
+
+    flags = 0
+    if opts.ignore_case:
+        flags |= re.I
+
+    try:
+        pattern = re.compile(args[0], flags)
+    except:
+        exit(1)
+    files = args[1:]
+
+    opts.curr_count = 0
+
+    if len(files) > 1 or opts.print_filename:
+        opts.print_filename = True
+
+    for f in files:
+        search(pattern, f, opts)