def test_Butterfly_is_identified_correctly(self):
lines = ["20140920 17:28:14 30084 befulton 20 62435 0 S 24215176 0 37768 24080384 92 4 14420 30 0.03 0.17 "
"4 00:00.20 0 6 519 0 203 1 0 0 1056 java -Xmx20G -Xms1G -jar /trinity/Butterfly/Butterfly.jar "
"-N 100000 -L 200 -F 500 -C /jobdir/trinity_out/chrysalis/Component_bins/Cbin5/c6058.graph "
"--max_number_of_paths_per_node=10 --path_reinforcement_distance=75 --triplet-lock"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['Butterfly'])
def test_build_datasets_adds_inchworm_to_line_dict(self):
lines = [
"20140919 11:08:49 44009 user 20 44008 0 R 10975748 0 10837764 10957692 92 128 3416 9 0.00 4.99 99 "
"01:33:35 0 0 0 0 0 0 0 0 1 /N/test/Inchworm/bin/inchworm --kmers jellyfish.kmers.fa --run_inchworm "
"-K 25 -L 25 --monitor 1"
]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['inchworm'])
def test_Butterfly_is_identified_correctly(self):
lines = [
"20140920 17:28:14 30084 befulton 20 62435 0 S 24215176 0 37768 24080384 92 4 14420 30 0.03 0.17 "
"4 00:00.20 0 6 519 0 203 1 0 0 1056 java -Xmx20G -Xms1G -jar /trinity/Butterfly/Butterfly.jar "
"-N 100000 -L 200 -F 500 -C /jobdir/trinity_out/chrysalis/Component_bins/Cbin5/c6058.graph "
"--max_number_of_paths_per_node=10 --path_reinforcement_distance=75 --triplet-lock"
]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['Butterfly'])
def test_Chrysalis_is_identified_correctly(self):
lines = ["20140920 11:29:54 49383 befulton 20 43684 0 S 18468 0 1464 300 92 236 3416 8 0.00 0.00 0 00:02.44 "
"0 0 0 0 0 0 0 0 0 /trinity/Chrysalis/Chrysalis "
"-i both.fa -iworm /jobdir/trinity_out/inchworm.K25.L25.fa.clipped.fa -o "
"/jobdir/trinity_out/chrysalis -cpu 16 -min_glue 2 "
"-min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 "
"-sort_buffer_size 20G -max_mem_reads 1000000 -strand 1 -paired -reads_for_pairs both.fa "
"-butterfly /trinity/Butterfly/Butterfly.jar"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['Chrysalis'])
def test_build_datasets_adds_bowtie_build_to_line_dict_if_no_path(self):
lines = ["20140919 11:11:24 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 "
"02:27.86 0 960 0 960 0 124 0 0 0 bowtie-build /N/test/trinity_out/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa",
"20140919 11:11:29 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
" 0 960 0 960 0 124 0 0 0 bowtie-build /N/trinity_out/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa",
"20140919 11:11:34 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
" 0 960 0 960 0 124 0 0 0 some_app /N/trinity_out/bowtie-build/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines[0:2], line_dict['bowtie-build'])
def test_Chrysalis_is_identified_correctly(self):
lines = [
"20140920 11:29:54 49383 befulton 20 43684 0 S 18468 0 1464 300 92 236 3416 8 0.00 0.00 0 00:02.44 "
"0 0 0 0 0 0 0 0 0 /trinity/Chrysalis/Chrysalis "
"-i both.fa -iworm /jobdir/trinity_out/inchworm.K25.L25.fa.clipped.fa -o "
"/jobdir/trinity_out/chrysalis -cpu 16 -min_glue 2 "
"-min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 "
"-sort_buffer_size 20G -max_mem_reads 1000000 -strand 1 -paired -reads_for_pairs both.fa "
"-butterfly /trinity/Butterfly/Butterfly.jar"
]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['Chrysalis'])
def test_build_datasets_adds_bowtie_build_to_line_dict_if_no_path(self):
lines = [
"20140919 11:11:24 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 "
"02:27.86 0 960 0 960 0 124 0 0 0 bowtie-build /N/test/trinity_out/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa",
"20140919 11:11:29 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
" 0 960 0 960 0 124 0 0 0 bowtie-build /N/trinity_out/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa",
"20140919 11:11:34 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
" 0 960 0 960 0 124 0 0 0 some_app /N/trinity_out/bowtie-build/jaccard_clip_workdir/iworm.fa "
"/N/trinity_out/jaccard_clip_workdir/iworm.fa"
]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines[0:2], line_dict['bowtie-build'])
def test_shell_c_commands_are_dropped(self):
lines = ["20140919 10:06:14 43812 befulton 20 43684 0 S 108160 0 1228 196 92 848 1832 1 0.00 0.00 0 00:00.00 " \
"0 0 0 0 0 0 0 0 0 sh -c /trinity/trinity-plugins/fastool/fastool --rev --illumina-trinity " \
"--to-fasta /jobdir/reads.left.fq >> left.fa"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(0, len(line_dict))
def test_build_datasets_adds_inchworm_to_line_dict(self):
lines = ["20140919 11:08:49 44009 user 20 44008 0 R 10975748 0 10837764 10957692 92 128 3416 9 0.00 4.99 99 "
"01:33:35 0 0 0 0 0 0 0 0 1 /N/test/Inchworm/bin/inchworm --kmers jellyfish.kmers.fa --run_inchworm "
"-K 25 -L 25 --monitor 1"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(lines, line_dict['inchworm'])
def test_build_datasets_returns_last_line_time_as_end_time(self):
lines = ["20140919 13:10:49\n",
"20140919 11:10:49\n",
"20140919 11:27:49\n"]
_, _, _, _, end_time = make_data_files.build_datasets(generate(lines))
self.assertEquals(['20140919', '11:27:49'], end_time)
def test_shell_c_commands_are_dropped(self):
lines = ["20140919 10:06:14 43812 befulton 20 43684 0 S 108160 0 1228 196 92 848 1832 1 0.00 0.00 0 00:00.00 " \
"0 0 0 0 0 0 0 0 0 sh -c /trinity/trinity-plugins/fastool/fastool --rev --illumina-trinity " \
"--to-fasta /jobdir/reads.left.fq >> left.fa"]
_, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
self.assertEquals(0, len(line_dict))
def test_build_datasets_returns_last_line_time_as_end_time(self):
lines = [
"20140919 13:10:49\n", "20140919 11:10:49\n", "20140919 11:27:49\n"
]
_, _, _, _, end_time = make_data_files.build_datasets(generate(lines))
self.assertEquals(['20140919', '11:27:49'], end_time)