[med-svn] [python-biotools] 01/01: Add missing script grepseq as quilt patch
Andreas Tille
tille at debian.org
Thu Mar 2 18:46:42 UTC 2017
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tille pushed a commit to branch master
in repository python-biotools.
commit 0847cc5893e80d1e98512a85eff14726724b5b16
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 2 16:51:38 2017 +0100
Add missing script grepseq as quilt patch
---
debian/patches/2to3_grepseq.patch | 35 +++++++++++
debian/patches/add_missing_grepseq.patch | 101 +++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/python3-biotools.install | 1 +
4 files changed, 139 insertions(+)
diff --git a/debian/patches/2to3_grepseq.patch b/debian/patches/2to3_grepseq.patch
new file mode 100644
index 0000000..22d5f2b
--- /dev/null
+++ b/debian/patches/2to3_grepseq.patch
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 02 Mar 2017 11:51:33 +0100
+Description: Fix Python3 errors by using 2to3
+
+--- a/grepseq
++++ b/grepseq
+@@ -14,7 +14,7 @@ def search(regex, filename, options):
+ cmx = options.max_count
+
+ if pfn and not cnt:
+- print '\n=======>', filename, '<=======\n'
++ print('\n=======>', filename, '<=======\n')
+
+ for seq in io.open(filename, 'r'):
+ in_name = snm and regex.search(seq.name + ' ' + seq.defline)
+@@ -22,16 +22,16 @@ def search(regex, filename, options):
+ if not inv and (in_name or in_seq):
+ options.curr_count += 1
+ if not cnt:
+- print seq
++ print(seq)
+ elif inv and not (in_name or in_seq):
+ options.curr_count += 1
+ if not cnt:
+- print seq
++ print(seq)
+ if cmx and options.curr_count > cmx:
+ break
+
+ if cnt:
+- print options.curr_count
++ print(options.curr_count)
+
+ if __name__ == '__main__':
+ optp = OptionParser(usage="%prog [options] <pattern> <files ...>")
diff --git a/debian/patches/add_missing_grepseq.patch b/debian/patches/add_missing_grepseq.patch
new file mode 100644
index 0000000..b834277
--- /dev/null
+++ b/debian/patches/add_missing_grepseq.patch
@@ -0,0 +1,101 @@
+Author: Andreas Tille <tille at 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)
diff --git a/debian/patches/series b/debian/patches/series
index 998d10f..43ec752 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
2to3.patch
+add_missing_grepseq.patch
+2to3_grepseq.patch
diff --git a/debian/python3-biotools.install b/debian/python3-biotools.install
new file mode 100644
index 0000000..158d51d
--- /dev/null
+++ b/debian/python3-biotools.install
@@ -0,0 +1 @@
+grepseq usr/bin
--
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