From 3951d31465a164e40223f4df32030d504702a46d Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 13:18:35 +0000 Subject: [PATCH 01/20] Check for xvfb-run --- kinfin.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/kinfin.py b/kinfin.py index 619edea..e748b39 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2100,13 +2100,17 @@ def check_that_ete_can_plot(self): sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") from ete3 import Tree t = Tree( "((a,b),c);" ) - try: - test_tree_f = join(getcwd(), "%s.this_is_a_test_tree.pdf" % (outprefix)) - t.render("test_tree_f.pdf", w=40, units="mm") - print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." - except: - print "[WARN] : ETE cannot connect to X server (X11). No tree will be rendered." - self.render_tree = False + test_tree_f = join(getcwd(), "%s.this_is_a_test_tree.pdf" % (outprefix)) + t.render("test_tree_f.pdf", w=40, units="mm") + print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." + self.render_tree = True + # try: + # test_tree_f = join(getcwd(), "%s.this_is_a_test_tree.pdf" % (outprefix)) + # t.render("test_tree_f.pdf", w=40, units="mm") + # print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." + # except: + # print "[WARN] : ETE cannot connect to X server (X11). No tree will be rendered." + # self.render_tree = False def check_fuzzy_count(self, target_count): if int(target_count) > 0: From 334997697e6921f8500f2cdfa1267847e9736608 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 13:23:04 +0000 Subject: [PATCH 02/20] Fixing xvfb-run compatibility ... --- kinfin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index e748b39..052c168 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2100,7 +2100,7 @@ def check_that_ete_can_plot(self): sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") from ete3 import Tree t = Tree( "((a,b),c);" ) - test_tree_f = join(getcwd(), "%s.this_is_a_test_tree.pdf" % (outprefix)) + test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") t.render("test_tree_f.pdf", w=40, units="mm") print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." self.render_tree = True From e78423ca30f10919258b21885584075349bd05ee Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 13:26:13 +0000 Subject: [PATCH 03/20] Fixing xvfb-run/ETE tests --- kinfin.py | 22 +++++++--------------- 1 file changed, 7 insertions(+), 15 deletions(-) diff --git a/kinfin.py b/kinfin.py index 052c168..4c478d5 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2101,16 +2101,13 @@ def check_that_ete_can_plot(self): from ete3 import Tree t = Tree( "((a,b),c);" ) test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") - t.render("test_tree_f.pdf", w=40, units="mm") - print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." - self.render_tree = True - # try: - # test_tree_f = join(getcwd(), "%s.this_is_a_test_tree.pdf" % (outprefix)) - # t.render("test_tree_f.pdf", w=40, units="mm") - # print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." - # except: - # print "[WARN] : ETE cannot connect to X server (X11). No tree will be rendered." - # self.render_tree = False + try: + t.render(test_tree_f, w=40, units="mm") + print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." + self.render_tree = True + except: + print "[WARN] : ETE cannot connect to X server (X11). No tree will be rendered." + self.render_tree = False def check_fuzzy_count(self, target_count): if int(target_count) > 0: @@ -2150,11 +2147,6 @@ def welcome_screen(): args = docopt(__doc__) # Sanitise input inputObj = InputObj(args) - if inputObj.tree_f: - try: - import ete3 - except: - sys.exit("[ERROR] : Module \'ete3\' was not found. Please install \'ete3\' using \'pip install ete3\'") # Input sane ... now we start print "[STATUS] - Starting analysis ..." From a161d8d223152636b022413fcc315238dac3c335 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 13:38:14 +0000 Subject: [PATCH 04/20] Fixing ete --- kinfin.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/kinfin.py b/kinfin.py index 4c478d5..7c9cd65 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2090,14 +2090,6 @@ def check_input_files(self): def check_that_ete_can_plot(self): if self.tree_f: - try: - import ete3 - except ImportError: - sys.exit("[ERROR] : Module \'ete3\' was not found. Please install \'ete3\' using \'pip install ete3\'\n/tPlotting of trees requires additional dependencies:\n\t- PyQt4\n\t") - try: - import PyQt4 - except ImportError: - sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") from ete3 import Tree t = Tree( "((a,b),c);" ) test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") @@ -2147,7 +2139,15 @@ def welcome_screen(): args = docopt(__doc__) # Sanitise input inputObj = InputObj(args) - + if inputObj.tree_f: + try: + import ete3 + except ImportError: + sys.exit("[ERROR] : Module \'ete3\' was not found. Please install \'ete3\' using \'pip install ete3\'\n/tPlotting of trees requires additional dependencies:\n\t- PyQt4\n\t") + try: + import PyQt4 + except ImportError: + sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") # Input sane ... now we start print "[STATUS] - Starting analysis ..." overall_start = time.time() From 6dae736cee2d97cba93bc2419643cddce147e741 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:02:29 +0000 Subject: [PATCH 05/20] ... --- kinfin.py | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/kinfin.py b/kinfin.py index 7c9cd65..ccc2360 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2070,20 +2070,20 @@ def check_input_files(self): if self.pfam_mapping: pfam_mapping_f = join(dirname(realpath(__file__)), "data/Pfam-A.clans.tsv.gz") if not isfile(pfam_mapping_f): - print "[WARN] : PFAM-ID file 'data/Pfam-A.clans.tsv.gz' not found." + print "[WARN] - PFAM-ID file 'data/Pfam-A.clans.tsv.gz' not found." remote_f = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz" retrieve_ftp(remote_f, pfam_mapping_f) self.pfam_mapping_f = pfam_mapping_f if self.ipr_mapping: ipr_mapping_f = join(dirname(realpath(__file__)), "data/entry.list") if not isfile(ipr_mapping_f): - print "[WARN] : IPR-ID file 'data/entry.list' not found." + print "[WARN] - IPR-ID file 'data/entry.list' not found." remote_f = "ftp://ftp.ebi.ac.uk/pub/databases/interpro/entry.list" retrieve_ftp(remote_f, ipr_mapping_f) self.ipr_mapping_f = ipr_mapping_f go_mapping_f = join(dirname(realpath(__file__)), "data/interpro2go") if not isfile(go_mapping_f): - print "[WARN] : GO-ID file, but 'data/interpro2go' not found." + print "[WARN] - GO-ID file, but 'data/interpro2go' not found." remote_f = "ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro2go" retrieve_ftp(remote_f, go_mapping_f) self.go_mapping_f = go_mapping_f @@ -2091,14 +2091,17 @@ def check_input_files(self): def check_that_ete_can_plot(self): if self.tree_f: from ete3 import Tree + try: + import PyQt4 + except ImportError: + sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") t = Tree( "((a,b),c);" ) test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") try: t.render(test_tree_f, w=40, units="mm") - print "[STATUS] : ETE can connect to X server (X11). Tree will be rendered." - self.render_tree = True + print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." except: - print "[WARN] : ETE cannot connect to X server (X11). No tree will be rendered." + print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." self.render_tree = False def check_fuzzy_count(self, target_count): @@ -2144,10 +2147,6 @@ def welcome_screen(): import ete3 except ImportError: sys.exit("[ERROR] : Module \'ete3\' was not found. Please install \'ete3\' using \'pip install ete3\'\n/tPlotting of trees requires additional dependencies:\n\t- PyQt4\n\t") - try: - import PyQt4 - except ImportError: - sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") # Input sane ... now we start print "[STATUS] - Starting analysis ..." overall_start = time.time() From 5085f095c35728c58ae90f71ea1a685f3c519c9a Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:03:43 +0000 Subject: [PATCH 06/20] ... --- kinfin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index ccc2360..148ddc2 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2095,9 +2095,9 @@ def check_that_ete_can_plot(self): import PyQt4 except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") - t = Tree( "((a,b),c);" ) test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") try: + t = Tree( "((a,b),c);" ) t.render(test_tree_f, w=40, units="mm") print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." except: From 2c9d53340400eb7a0970162a75146254f90a7592 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:05:11 +0000 Subject: [PATCH 07/20] ... --- kinfin.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/kinfin.py b/kinfin.py index 148ddc2..7e4ab74 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2090,14 +2090,13 @@ def check_input_files(self): def check_that_ete_can_plot(self): if self.tree_f: - from ete3 import Tree try: import PyQt4 except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") try: - t = Tree( "((a,b),c);" ) + t = ete3.Tree( "((a,b),c);" ) t.render(test_tree_f, w=40, units="mm") print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." except: From 0acf87a8a74992cd018f8a5ed12aaee6492bdc62 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:07:15 +0000 Subject: [PATCH 08/20] ... --- kinfin.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/kinfin.py b/kinfin.py index 7e4ab74..b91dca7 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2095,13 +2095,12 @@ def check_that_ete_can_plot(self): except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") - try: - t = ete3.Tree( "((a,b),c);" ) - t.render(test_tree_f, w=40, units="mm") - print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." - except: - print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." - self.render_tree = False + t = ete3.Tree( "((a,b),c);" ) + t.render(test_tree_f, w=40, units="mm") + print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." + #except: + # print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." + # self.render_tree = False def check_fuzzy_count(self, target_count): if int(target_count) > 0: From 51edff328d7af4e15e8df7f3e21fdbe57732934c Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:10:23 +0000 Subject: [PATCH 09/20] ... --- kinfin.py | 1 + 1 file changed, 1 insertion(+) diff --git a/kinfin.py b/kinfin.py index b91dca7..c18fbb9 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2141,6 +2141,7 @@ def welcome_screen(): # Sanitise input inputObj = InputObj(args) if inputObj.tree_f: + print "[STATUS] - Tree specified : %s" % (inputObj.tree_f) try: import ete3 except ImportError: From e270f6631fa05a68bad5bceb52644d8c8a44fd22 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:12:03 +0000 Subject: [PATCH 10/20] ... --- kinfin.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index c18fbb9..92acc54 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2090,6 +2090,10 @@ def check_input_files(self): def check_that_ete_can_plot(self): if self.tree_f: + try: + import ete3 + except ImportError: + sys.exit("[ERROR] : Module \'ete3\' was not found. Please install \'ete3\' using \'pip install ete3\'\n/tPlotting of trees requires additional dependencies:\n\t- PyQt4\n\t") try: import PyQt4 except ImportError: @@ -2138,7 +2142,6 @@ def welcome_screen(): __version__ = "0.8.2" welcome_screen() args = docopt(__doc__) - # Sanitise input inputObj = InputObj(args) if inputObj.tree_f: print "[STATUS] - Tree specified : %s" % (inputObj.tree_f) From 29c6e4997a2007822c22bf8c614bcb6a8d050a51 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:35:23 +0000 Subject: [PATCH 11/20] ... --- kinfin.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/kinfin.py b/kinfin.py index 92acc54..988be7d 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2098,13 +2098,15 @@ def check_that_ete_can_plot(self): import PyQt4 except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") - test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") - t = ete3.Tree( "((a,b),c);" ) - t.render(test_tree_f, w=40, units="mm") - print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." - #except: - # print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." - # self.render_tree = False + try: + test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") + t = ete3.Tree( "((a,b),c);" ) + t.render(test_tree_f, w=40, units="mm") + print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." + os.remove(test_tree_f) + except: + print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." + self.render_tree = False def check_fuzzy_count(self, target_count): if int(target_count) > 0: From a3071a3b5ecb74d458508a28fcdb7734b45ed350 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:36:22 +0000 Subject: [PATCH 12/20] ... --- kinfin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index 988be7d..3bbf418 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2103,10 +2103,10 @@ def check_that_ete_can_plot(self): t = ete3.Tree( "((a,b),c);" ) t.render(test_tree_f, w=40, units="mm") print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." - os.remove(test_tree_f) except: print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." self.render_tree = False + os.remove(test_tree_f) def check_fuzzy_count(self, target_count): if int(target_count) > 0: From 1c67ed711a19e701404c4e2f7abc343b5826c56c Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:36:56 +0000 Subject: [PATCH 13/20] ... --- kinfin.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/kinfin.py b/kinfin.py index 3bbf418..5edda5d 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2098,14 +2098,15 @@ def check_that_ete_can_plot(self): import PyQt4 except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") + + test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") + t = ete3.Tree( "((a,b),c);" ) try: - test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") - t = ete3.Tree( "((a,b),c);" ) t.render(test_tree_f, w=40, units="mm") print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." except: - print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." self.render_tree = False + print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." os.remove(test_tree_f) def check_fuzzy_count(self, target_count): From 8e378225cfd41370b6217e18c1f480a0a14e7068 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:37:45 +0000 Subject: [PATCH 14/20] ... --- kinfin.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kinfin.py b/kinfin.py index 5edda5d..f9e6451 100755 --- a/kinfin.py +++ b/kinfin.py @@ -53,7 +53,7 @@ from __future__ import division import sys from os.path import isfile, join, exists, realpath, dirname -from os import getcwd, mkdir +from os import getcwd, mkdir, remove import shutil import random import time @@ -2107,7 +2107,7 @@ def check_that_ete_can_plot(self): except: self.render_tree = False print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." - os.remove(test_tree_f) + remove(test_tree_f) def check_fuzzy_count(self, target_count): if int(target_count) > 0: From beaf8dcdbef867cf318e0a6933288bf4fdf75b97 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:39:16 +0000 Subject: [PATCH 15/20] ... --- kinfin.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index f9e6451..4761a18 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2102,7 +2102,8 @@ def check_that_ete_can_plot(self): test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") t = ete3.Tree( "((a,b),c);" ) try: - t.render(test_tree_f, w=40, units="mm") + a = t.render(test_tree_f, w=40, units="mm") + print a print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." except: self.render_tree = False From 2a258ffbf66bcdcf1eeec1b1533ef4b4d275e76e Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:43:03 +0000 Subject: [PATCH 16/20] ... --- kinfin.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index 4761a18..72eca67 100755 --- a/kinfin.py +++ b/kinfin.py @@ -53,7 +53,7 @@ from __future__ import division import sys from os.path import isfile, join, exists, realpath, dirname -from os import getcwd, mkdir, remove +from os import getcwd, mkdir, remove, environ import shutil import random import time @@ -2101,6 +2101,7 @@ def check_that_ete_can_plot(self): test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") t = ete3.Tree( "((a,b),c);" ) + print environ['DISPLAY'] try: a = t.render(test_tree_f, w=40, units="mm") print a From bce1855d94b491c802ed4cb0c04b6976c63347bf Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:47:12 +0000 Subject: [PATCH 17/20] .... --- kinfin.py | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/kinfin.py b/kinfin.py index 72eca67..c63e31d 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2099,17 +2099,20 @@ def check_that_ete_can_plot(self): except ImportError: sys.exit("[ERROR] : PyQt4 is not installed. Please install PyQt4") - test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") - t = ete3.Tree( "((a,b),c);" ) - print environ['DISPLAY'] - try: - a = t.render(test_tree_f, w=40, units="mm") - print a - print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." - except: + if 'DISPLAY' in environ: + print "[STATUS] - X server seems to be present..." + test_tree_f = join(getcwd(), "this_is_a_test_tree.pdf") + t = ete3.Tree( "((a,b),c);" ) + try: + a = t.render(test_tree_f, w=40, units="mm") + print "[STATUS] - ETE can connect to X server (X11). Tree will be rendered." + except: + self.render_tree = False + print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." + remove(test_tree_f) + else: + print "[STATUS] - No X server seems to be present. ETE can't render the tree. Consider using \'xvfb-run\' ..." self.render_tree = False - print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." - remove(test_tree_f) def check_fuzzy_count(self, target_count): if int(target_count) > 0: From dcc9eeafcab033778e7e56c98e9f227cdc73ed09 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:49:19 +0000 Subject: [PATCH 18/20] ... --- kinfin.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/kinfin.py b/kinfin.py index c63e31d..6155e87 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2111,7 +2111,7 @@ def check_that_ete_can_plot(self): print "[WARN] - ETE cannot connect to X server (X11). No tree will be rendered." remove(test_tree_f) else: - print "[STATUS] - No X server seems to be present. ETE can't render the tree. Consider using \'xvfb-run\' ..." + print "[STATUS] - No X server found. ETE can't render the tree. Consider using \'xvfb-run\' ..." self.render_tree = False def check_fuzzy_count(self, target_count): @@ -2152,7 +2152,6 @@ def welcome_screen(): args = docopt(__doc__) inputObj = InputObj(args) if inputObj.tree_f: - print "[STATUS] - Tree specified : %s" % (inputObj.tree_f) try: import ete3 except ImportError: From 360b723ac88f7f5170fc4053b86d1e93244ea033 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Sun, 26 Feb 2017 15:51:49 +0000 Subject: [PATCH 19/20] v0.8.3 - Fixed X11-display-check for ETE3 when passing tree-file as argument --- kinfin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kinfin.py b/kinfin.py index 6155e87..57c6e75 100755 --- a/kinfin.py +++ b/kinfin.py @@ -2147,7 +2147,7 @@ def welcome_screen(): if __name__ == "__main__": - __version__ = "0.8.2" + __version__ = "0.8.3" welcome_screen() args = docopt(__doc__) inputObj = InputObj(args) From d4bc9cba5df9bdf13e9f4ceacfd4146dc4d6e721 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Mon, 13 Mar 2017 13:14:16 +0000 Subject: [PATCH 20/20] Feature - Improved Error message for proteins in clustering from undeclared proteomes in SpeciesClassification file --- kinfin.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kinfin.py b/kinfin.py index 57c6e75..66798bd 100755 --- a/kinfin.py +++ b/kinfin.py @@ -1900,8 +1900,8 @@ def __init__(self, cluster_id, protein_ids): self.protein_count = len(protein_ids) try: self.proteomes_by_protein_id = {protein_id : proteinCollection.proteinObjs_by_protein_id[protein_id].proteome_id for protein_id in protein_ids} - except KeyError: - sys.exit("[ERROR] - Proteins in clustering belong to proteomes that are not present in the SpeciesClassification-file. Please add those proteoemes or recluster by omitting these proteomes.") + except KeyError as e: + sys.exit("[ERROR] - Protein %s in clustering belong to proteomes that are not present in the SpeciesClassification-file. Please add those proteoemes or recluster by omitting these proteomes." % (e.args[0])) self.proteome_ids_list = self.proteomes_by_protein_id.values() self.protein_count_by_proteome_id = Counter(self.proteome_ids_list)