From 555db4244a1c26e58750ef2f22c0559a24374303 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 8 Jul 2020 09:14:16 +0200 Subject: [PATCH] remove uncorrect_ini_file folder --- pygenometracks/tests/test_bed_and_gtf_tracks.py | 12 ++++++------ pygenometracks/tests/test_checker.py | 2 +- .../test_data/uncorrect_ini_files/bed_as_gtf.ini | 7 ------- .../tests/test_data/uncorrect_ini_files/empty.bed | 0 .../test_data/uncorrect_ini_files/gtf_as_bed.ini | 7 ------- .../test_data/uncorrect_ini_files/test_tracks_1.ini | 3 --- .../test_data/uncorrect_ini_files/test_tracks_10.ini | 4 ---- .../test_data/uncorrect_ini_files/test_tracks_11.ini | 3 --- .../test_data/uncorrect_ini_files/test_tracks_2.ini | 3 --- .../test_data/uncorrect_ini_files/test_tracks_3.ini | 3 --- .../test_data/uncorrect_ini_files/test_tracks_4.ini | 3 --- .../test_data/uncorrect_ini_files/test_tracks_5.ini | 5 ----- .../test_data/uncorrect_ini_files/test_tracks_6.ini | 5 ----- .../test_data/uncorrect_ini_files/test_tracks_7.ini | 5 ----- .../test_data/uncorrect_ini_files/test_tracks_8.ini | 5 ----- .../test_data/uncorrect_ini_files/test_tracks_9.ini | 5 ----- 16 files changed, 7 insertions(+), 65 deletions(-) delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/bed_as_gtf.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/empty.bed delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/gtf_as_bed.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_1.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_10.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_11.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_2.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_3.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_4.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_5.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_6.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_7.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_8.ini delete mode 100644 pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_9.ini diff --git a/pygenometracks/tests/test_bed_and_gtf_tracks.py b/pygenometracks/tests/test_bed_and_gtf_tracks.py index 7194a0b9..605c88f8 100644 --- a/pygenometracks/tests/test_bed_and_gtf_tracks.py +++ b/pygenometracks/tests/test_bed_and_gtf_tracks.py @@ -486,25 +486,25 @@ wrong_track = """ [test gtf] -file = ../dm3_subset_BDGP5.78_gtf.dat +file = dm3_subset_BDGP5.78_gtf.dat height = 10 title = gtf from ensembl (with dat extension) fontsize = 12 file_type = bed """ -with open(os.path.join(ROOT, "uncorrect_ini_files", "gtf_as_bed.ini"), 'w') as fh: +with open(os.path.join(ROOT, "gtf_as_bed.ini"), 'w') as fh: fh.write(wrong_track) wrong_track = """ [test bed] -file = ../dm3_genes.bed.gz +file = dm3_genes.bed.gz height = 10 title = bed file fontsize = 12 file_type = gtf """ -with open(os.path.join(ROOT, "uncorrect_ini_files", "bed_as_gtf.ini"), 'w') as fh: +with open(os.path.join(ROOT, "bed_as_gtf.ini"), 'w') as fh: fh.write(wrong_track) browser_tracks = """ @@ -762,7 +762,7 @@ def test_gtf_as_bed(): args = "--tracks {0} --region X:3100000-3200000 "\ "--trackLabelFraction 0.2 --width 38 --dpi 130 " \ "--trackLabelHAlign right --outFileName {1}" \ - "".format(os.path.join(ROOT, "uncorrect_ini_files", "gtf_as_bed.ini"), + "".format(os.path.join(ROOT, "gtf_as_bed.ini"), outfile.name).split() try: pygenometracks.plotTracks.main(args) @@ -779,7 +779,7 @@ def test_bed_as_gtf(): args = "--tracks {0} --region X:3100000-3200000 "\ "--trackLabelFraction 0.2 --width 38 --dpi 130 " \ "--trackLabelHAlign right --outFileName {1}" \ - "".format(os.path.join(ROOT, "uncorrect_ini_files", "bed_as_gtf.ini"), + "".format(os.path.join(ROOT, "bed_as_gtf.ini"), outfile.name).split() try: pygenometracks.plotTracks.main(args) diff --git a/pygenometracks/tests/test_checker.py b/pygenometracks/tests/test_checker.py index 533b48a3..71345dc6 100644 --- a/pygenometracks/tests/test_checker.py +++ b/pygenometracks/tests/test_checker.py @@ -11,7 +11,7 @@ ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), - "test_data", "uncorrect_ini_files") + "test_data") test_tracks_1 = """ [vlines] diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/bed_as_gtf.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/bed_as_gtf.ini deleted file mode 100644 index dbfaf2d5..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/bed_as_gtf.ini +++ /dev/null @@ -1,7 +0,0 @@ - -[test bed] -file = ../dm3_genes.bed.gz -height = 10 -title = bed file -fontsize = 12 -file_type = gtf diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/empty.bed b/pygenometracks/tests/test_data/uncorrect_ini_files/empty.bed deleted file mode 100644 index e69de29b..00000000 diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/gtf_as_bed.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/gtf_as_bed.ini deleted file mode 100644 index 8d103b01..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/gtf_as_bed.ini +++ /dev/null @@ -1,7 +0,0 @@ - -[test gtf] -file = ../dm3_subset_BDGP5.78_gtf.dat -height = 10 -title = gtf from ensembl (with dat extension) -fontsize = 12 -file_type = bed diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_1.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_1.ini deleted file mode 100644 index 705f7e91..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_1.ini +++ /dev/null @@ -1,3 +0,0 @@ - -[vlines] -type = vlines diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_10.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_10.ini deleted file mode 100644 index e0c80190..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_10.ini +++ /dev/null @@ -1,4 +0,0 @@ - -[inexisting file] -file_type = bed -file = FileWhichDoesNotExists.txt diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_11.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_11.ini deleted file mode 100644 index 31f73d7e..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_11.ini +++ /dev/null @@ -1,3 +0,0 @@ - -[unguessable file] -file = FileWhichDoesNotExists.unknownextension diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_2.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_2.ini deleted file mode 100644 index dc92a629..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_2.ini +++ /dev/null @@ -1,3 +0,0 @@ - -[wrong file_type] -file_type = newFileTypeIJustInvented diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_3.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_3.ini deleted file mode 100644 index fbda0f37..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_3.ini +++ /dev/null @@ -1,3 +0,0 @@ - -[undetermined section] -title = I do not know what diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_4.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_4.ini deleted file mode 100644 index 35e687cd..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_4.ini +++ /dev/null @@ -1,3 +0,0 @@ - -[missing necessary option] -file_type = bed diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_5.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_5.ini deleted file mode 100644 index 2c3c1099..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_5.ini +++ /dev/null @@ -1,5 +0,0 @@ - -[problem with boolean] -file_type = bed -file = empty.bed -labels = 2 diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_6.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_6.ini deleted file mode 100644 index 2a56ccf5..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_6.ini +++ /dev/null @@ -1,5 +0,0 @@ - -[problem with float] -file_type = bed -file = empty.bed -max_value = a diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_7.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_7.ini deleted file mode 100644 index 6a7b1c52..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_7.ini +++ /dev/null @@ -1,5 +0,0 @@ - -[problem with float range] -file_type = bed -file = empty.bed -fontsize = -2 diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_8.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_8.ini deleted file mode 100644 index e707d4a2..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_8.ini +++ /dev/null @@ -1,5 +0,0 @@ - -[problem with integer] -file_type = bed -file = empty.bed -gene_rows = 1a2 diff --git a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_9.ini b/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_9.ini deleted file mode 100644 index e8b441fa..00000000 --- a/pygenometracks/tests/test_data/uncorrect_ini_files/test_tracks_9.ini +++ /dev/null @@ -1,5 +0,0 @@ - -[problem with integer range] -file_type = bed -file = empty.bed -gene_rows = -2