def test_prettyprocess_combines_sort_and_binsort(self):
line = "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 /bin/sort"
self.assertEquals("sort", make_data_files.prettyprocess(line))
line = "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 sort"
self.assertEquals("sort", make_data_files.prettyprocess(line))
def test_Samtools_identified_with_verb(self):
line = "20141008 01:51:30 14984 befulton 20 14982 0 S 17752 0 820 200 92 384 2664 2 0.00 0.00 0 00:00.00 99" \
" 0 1 0 2 0 0 0 61 samtools view -F4 -Sb -"
self.assertEquals("samtools_view", make_data_files.prettyprocess(line))
line = "20141008 01:51:30 14985 befulton 20 14982 0 S 17748 0 740 196 92 384 2664 16 0.00 0.00 0 00:00.00 26" \
" 0 1 0 2 0 0 0 59 samtools sort -no - -"
self.assertEquals("samtools_sort", make_data_files.prettyprocess(line))
def test_prettyprocess_combines_sort_and_binsort(self):
line = "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 /bin/sort"
self.assertEquals("sort", make_data_files.prettyprocess(line))
line = "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 sort"
self.assertEquals("sort", make_data_files.prettyprocess(line))
def test_Samtools_identified_with_verb(self):
line = "20141008 01:51:30 14984 befulton 20 14982 0 S 17752 0 820 200 92 384 2664 2 0.00 0.00 0 00:00.00 99" \
" 0 1 0 2 0 0 0 61 samtools view -F4 -Sb -"
self.assertEquals("samtools_view", make_data_files.prettyprocess(line))
line = "20141008 01:51:30 14985 befulton 20 14982 0 S 17748 0 740 196 92 384 2664 16 0.00 0.00 0 00:00.00 26" \
" 0 1 0 2 0 0 0 59 samtools sort -no - -"
self.assertEquals("samtools_sort", make_data_files.prettyprocess(line))
def test_Unknown_apps_in_Chrysalis_directory_are_not_Chrysalis(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/new_app " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("new_app_unknown",
make_data_files.prettyprocess(line))
def test_Unrecognized_gives_binary_and_unknown(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/new_app/bin/new_app " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("new_app_unknown",
make_data_files.prettyprocess(line))
def test_GraphFromFasta_identified(self):
line = "20141008 04:38:10 15672 befulton 20 15671 0 R 91636 0 11216 73412 92 292 3416 1 0.01 5.18 103" \
" 00:05.19 0 0 1342 0 337 3 0 0 579 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/GraphFromFasta " \
"-i /dev/shm/trinity72/trinity_out/inchworm.K25.L25.fa -r both.fa -min_contig_length 200 -min_glue 2 " \
"-glue_factor 0.05 -min_iso_ratio 0.05 -t 32 -k 24 -kk 48 -strand -scaffolding iworm_scaffolds.txt"
self.assertEquals("GraphFromFasta", make_data_files.prettyprocess(line))
def test_GraphFromFasta_identified(self):
line = "20141008 04:38:10 15672 befulton 20 15671 0 R 91636 0 11216 73412 92 292 3416 1 0.01 5.18 103" \
" 00:05.19 0 0 1342 0 337 3 0 0 579 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/GraphFromFasta " \
"-i /dev/shm/trinity72/trinity_out/inchworm.K25.L25.fa -r both.fa -min_contig_length 200 -min_glue 2 " \
"-glue_factor 0.05 -min_iso_ratio 0.05 -t 32 -k 24 -kk 48 -strand -scaffolding iworm_scaffolds.txt"
self.assertEquals("GraphFromFasta",
make_data_files.prettyprocess(line))
def test_Jellyfish_identified(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/jellyfish/bin/jellyfish " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("jellyfish", make_data_files.prettyprocess(line))
def test_sort(self):
line = "20140919 16:06:24 45210 befulton 20 45209 0 R 973936 0 966268 965740 92 88 1824 10 1.96 0.94 58 " \
"04:26.85 0 188211 178646 188416 82 92 0 0 0 sort -T . -S 2G -k 1,1 -k 3,3 right_fa.sam"
self.assertEquals("sort", make_data_files.prettyprocess(line))
def test_Unknown_apps_in_Chrysalis_directory_are_not_Chrysalis(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/new_app " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("new_app_unknown", make_data_files.prettyprocess(line))
def test_Unrecognized_gives_binary_and_unknown(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/new_app/bin/new_app " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("new_app_unknown", make_data_files.prettyprocess(line))
def test_sort(self):
line = "20140919 16:06:24 45210 befulton 20 45209 0 R 973936 0 966268 965740 92 88 1824 10 1.96 0.94 58 " \
"04:26.85 0 188211 178646 188416 82 92 0 0 0 sort -T . -S 2G -k 1,1 -k 3,3 right_fa.sam"
self.assertEquals("sort", make_data_files.prettyprocess(line))
def test_Jellyfish_identified(self):
line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
" 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
"/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/jellyfish/bin/jellyfish " \
"count -t 32 -m 25 -s 1380200998 both.fa"
self.assertEquals("jellyfish", make_data_files.prettyprocess(line))
