[med-svn] [Git][med-team/gfapy][master] 3 commits: New upstream version 1.2.1+dfsg
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Sun Nov 14 10:13:25 GMT 2021
Sascha Steinbiss pushed to branch master at Debian Med / gfapy
Commits:
995ef4ed by Sascha Steinbiss at 2021-11-14T11:07:40+01:00
New upstream version 1.2.1+dfsg
- - - - -
7832bc30 by Sascha Steinbiss at 2021-11-14T11:07:41+01:00
Update upstream source from tag 'upstream/1.2.1+dfsg'
Update to upstream version '1.2.1+dfsg'
with Debian dir 0c800d1dfba586485a2a5a8156159dcee50b2b68
- - - - -
e4735e65 by Sascha Steinbiss at 2021-11-14T11:13:00+01:00
new upstream release
- - - - -
13 changed files:
- CHANGES.txt
- bin/gfapy-mergelinear
- debian/changelog
- doc/conf.py
- gfapy/field/oriented_identifier_list_gfa1.py
- gfapy/graph_operations/linear_paths.py
- gfapy/line/edge/link/canonical.py
- gfapy/line/group/path/captured_path.py
- gfapy/line/group/path/references.py
- setup.py
- tests/test_api_linear_paths.py
- + tests/testdata/linear_merging.6.gfa
- + tests/testdata/linear_merging.6.merged.gfa
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,8 @@
+== 1.2.1 ==
+
+- fixed an issue with linear path merging (issue 21)
+- GFA1 paths can contain a single segment only (issue 22)
+
== 1.2.0 ==
- fixed all open issues
=====================================
bin/gfapy-mergelinear
=====================================
@@ -16,6 +16,8 @@ op.add_argument("--no-progress", '-p', help="do not show progress log",
action="store_false", dest="progress")
op.add_argument("--quiet", '-q', help="suppress output", action="store_false",
dest="output")
+op.add_argument("--short", help="use short names for merged segments",
+ action="store_true")
op.add_argument("--vlevel", help="validation level", default=0, type=int)
op.add_argument('--version', action='version', version='%(prog)s 1.0')
opts = op.parse_args()
@@ -30,8 +32,12 @@ if opts.redundant:
for cc in gfa.connected_components():
if len(cc) == 1:
gfa.segment(cc[0]).disconnect()
+if opts.short:
+ merged_name="short"
+else:
+ merged_name=None
gfa.merge_linear_paths(redundant_junctions=opts.redundant,
enable_tracking=False,
- merged_name="short")
+ merged_name=merged_name)
if opts.output:
print(gfa)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+gfapy (1.2.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 14 Nov 2021 11:08:01 +0100
+
gfapy (1.2.0+dfsg-2) unstable; urgency=medium
* Fix watchfile to check /tags.
=====================================
doc/conf.py
=====================================
@@ -66,7 +66,7 @@ master_doc = 'index'
# General information about the project.
project = 'Gfapy'
-copyright = '2017, Giorgio Gonnella and others (see CONTRIBUTORS)'
+copyright = '2017--2021, Giorgio Gonnella and others (see CONTRIBUTORS)'
author = 'Giorgio Gonnella and others (see CONTRIBUTORS)'
# The version info for the project you're documenting, acts as replacement for
@@ -76,7 +76,7 @@ author = 'Giorgio Gonnella and others (see CONTRIBUTORS)'
# The short X.Y version.
version = '1.2'
# The full version, including alpha/beta/rc tags.
-release = '1.2.0'
+release = '1.2.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
=====================================
gfapy/field/oriented_identifier_list_gfa1.py
=====================================
@@ -10,14 +10,14 @@ def decode(string):
return unsafe_decode(string)
def validate_encoded(string):
- if not re.match(r"^[!-)+-<>-~][!-~]*[+-](,[!-)+-<>-~][!-~]*[+-])+$", string):
+ if not re.match(r"^[!-)+-<>-~][!-~]*[+-](,[!-)+-<>-~][!-~]*[+-])*$", string):
raise gfapy.FormatError(
"{} is not a valid list of GFA1 segment names ".format(repr(string))+
"and orientations\n"+
"(the segment names must match [!-)+-<>-~][!-~]*;\n"+
" the orientations must be + or -;\n"+
" the list must be comma-separated "+
- "NameOrient,NameOrient[,NameOrient...])")
+ "NameOrient[,NameOrient...])")
def validate_decoded(iterable):
for elem in iterable:
=====================================
gfapy/graph_operations/linear_paths.py
=====================================
@@ -348,8 +348,10 @@ class LinearPaths:
return merged, first_reversed, last_reversed
def __link_merged(self, merged_name, segment_end, is_reversed):
- for l in self.segment(segment_end.segment).dovetails_of_end(
- segment_end.end_type):
+ to_disconnect = self.segment(segment_end.segment).dovetails_of_end(
+ segment_end.end_type)
+ to_add = []
+ for l in to_disconnect:
l2 = l.clone()
if l2.to_segment == segment_end.segment:
l2.to_segment = merged_name
@@ -359,6 +361,10 @@ class LinearPaths:
l2.from_segment = merged_name
if is_reversed:
l2.from_orient = gfapy.invert(l2.from_orient)
+ to_add.append(l2)
+ for l in to_disconnect:
l.disconnect()
- self.add_line(l2)
+ for l in to_add:
+ self.add_line(l)
+
=====================================
gfapy/line/edge/link/canonical.py
=====================================
@@ -48,3 +48,5 @@ class Canonical:
"""
if not self.is_canonical():
return self.complement()
+ else:
+ return self()
=====================================
gfapy/line/group/path/captured_path.py
=====================================
@@ -28,11 +28,14 @@ class CapturedPath:
"Line is not connected to a GFA instance\n"+
"Line: {}".format(self))
retval = []
- for i in range(len(self.segment_names) - 1):
- retval.append(self.segment_names[i])
- retval.append(self.links[i])
- retval.append(self.segment_names[-1])
- if len(self.segment_names) == len(self.links):
- retval.append(self.links[-1])
+ if len(self.segment_names) == 1:
retval.append(self.segment_names[0])
+ else:
+ for i in range(len(self.segment_names) - 1):
+ retval.append(self.segment_names[i])
+ retval.append(self.links[i])
+ retval.append(self.segment_names[-1])
+ if len(self.segment_names) == len(self.links):
+ retval.append(self.links[-1])
+ retval.append(self.segment_names[0])
return retval
=====================================
gfapy/line/group/path/references.py
=====================================
@@ -13,6 +13,8 @@ class References:
An array, which elements are 3-tuples
(from oriented segment, to oriented segment, cigar)
"""
+ if len(self.segment_names) == 1:
+ return []
has_undef_overlaps = self._undef_overlaps()
retval = []
is_circular = self.is_circular()
=====================================
setup.py
=====================================
@@ -9,7 +9,7 @@ if not sys.version_info[0] == 3:
sys.exit("Sorry, only Python 3 is supported")
setup(name='gfapy',
- version='1.2.0',
+ version='1.2.1',
description='Library for handling data in the GFA1 and GFA2 formats',
long_description=readme(),
url='https://github.com/ggonnella/gfapy',
=====================================
tests/test_api_linear_paths.py
=====================================
@@ -47,6 +47,15 @@ class TestAPILinearPaths(unittest.TestCase):
lps.add(" ".join([s.name for s in lp]))
self.assertEqual({"1 19 18", "11 9 12", "22 16 20 21 23"}, lps)
+ def test_linear_path_merge_6(self):
+ gfa = gfapy.Gfa.from_file("tests/testdata/linear_merging.6.gfa")
+ expected = gfapy.Gfa.from_file("tests/testdata/linear_merging.6.merged.gfa")
+ gfa.merge_linear_paths()
+ self.assertEqual(set(gfa.segment_names), set(expected.segment_names))
+ dovetails_gfa = [str(l) for l in gfa.dovetails].sort()
+ dovetails_expected = [str(l) for l in expected.dovetails].sort()
+ self.assertEqual(dovetails_gfa, dovetails_expected)
+
def test_linear_path_blunt_ends(self):
for sfx in ["gfa1", "gfa2"]:
gfa = gfapy.Gfa.from_file("tests/testdata/linear_blunt."+"{}".format(sfx))
=====================================
tests/testdata/linear_merging.6.gfa
=====================================
@@ -0,0 +1,27 @@
+S A TTTTTCCCCCGGGGGGGGGGNCCCCCCCCCCTTTTTAAAAA LN:i:41
+S B AAAAAAAAAAGGGGGGGGGGNCCCCCCCCCCGGGGGAAAAA LN:i:41
+S C CCCCCCCCCCGGGGGGGGGGNCCCCCCCCCCTTTTTTTTTT LN:i:41
+S D TTTTTAAAAACCCCCCCCCCNAAAAAAAAAAAAAAATTTTT LN:i:41
+S E TTTTTAAAAAGGGGGGGGGGNCCCCCCCCCCCCCCCGGGGG LN:i:41
+S F AAAAAAAAAACCCCCCCCCCNAAAAAAAAAAAAAAATTTTT LN:i:41
+S X1 AAAAATTTTT LN:i:10
+S X2 AAAAATTTTT LN:i:10
+S X3 AAAAATTTTT LN:i:10
+S X4 AAAAATTTTT LN:i:10
+S X5 AAAAATTTTT LN:i:10
+S X6 AAAAATTTTT LN:i:10
+S X7 AAAAATTTTT LN:i:10
+S X8 AAAAATTTTT LN:i:10
+L B + A - 5M
+L B - C - 5M
+L C - D - 5M
+L D - E - 5M
+L E - F + 5M
+L A - X1 - 5M
+L A - X2 + 5M
+L X3 + A + 5M
+L X4 - A + 5M
+L F + X5 - 5M
+L F + X6 + 5M
+L X7 + F - 5M
+L X8 - F - 5M
=====================================
tests/testdata/linear_merging.6.merged.gfa
=====================================
@@ -0,0 +1,17 @@
+S A_B_C_D_E_F TTTTTCCCCCGGGGGGGGGGNCCCCCCCCCCTTTTTAAAAACCCCCGGGGGGGGGGNCCCCCCCCCCTTTTTTTTTTAAAAAGGGGGGGGGGNCCCCCCCCCCGGGGGGGGGGTTTTTTTTTTTTTTTNGGGGGGGGGGTTTTTAAAAAGGGGGGGGGGGGGGGNCCCCCCCCCCTTTTTAAAAAAAAAACCCCCCCCCCNAAAAAAAAAAAAAAATTTTT LN:i:221
+S X1 AAAAATTTTT LN:i:10
+S X2 AAAAATTTTT LN:i:10
+S X3 AAAAATTTTT LN:i:10
+S X4 AAAAATTTTT LN:i:10
+S X5 AAAAATTTTT LN:i:10
+S X6 AAAAATTTTT LN:i:10
+S X7 AAAAATTTTT LN:i:10
+S X8 AAAAATTTTT LN:i:10
+L A_B_C_D_E_F + X6 + 5M
+L A_B_C_D_E_F + X8 + 5M
+L X1 + A_B_C_D_E_F + 5M
+L X2 - A_B_C_D_E_F + 5M
+L X3 + A_B_C_D_E_F + 5M
+L X4 - A_B_C_D_E_F + 5M
+L X5 + A_B_C_D_E_F - 5M
+L X7 + A_B_C_D_E_F - 5M
View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/compare/6371fbe0eb318909cb9e28dd75a1a42b91371cde...e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4
--
View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/compare/6371fbe0eb318909cb9e28dd75a1a42b91371cde...e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4
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