Test
##Environment
- add script folder to your PATH by:
- type, from this folder, every time you open a new terminal
source enable.sh
- add (only once) cnidaria/scripts to your $HOME/.bashrc and restart (only once) your terminal
echo "export PATH=$PWD/scripts:$PATH" >> $HOME/.bashrc
##Run Either inside Docker or in your own installation:
make testIt will download 14 fungi genomes, extract their 21-mers and run cnidaria on it. The test takes approx. 30 min to run The raw data amounts to 293 Mb The Jellyfish data amounts to 2.0 Gb The Cnidaria data amounts to 1.7 Mb
The output should be: Input fasta and Jellyfish databases:
$ du -ah data
29M data/Aspergillus_fumigatus/Aspergillus_fumigatus.fasta
4.0K data/Aspergillus_fumigatus/21.jf.timming
189M data/Aspergillus_fumigatus/21.jf
217M data/Aspergillus_fumigatus
30M data/Aspergillus_nidulans/Aspergillus_nidulans.fasta
4.0K data/Aspergillus_nidulans/21.jf.timming
197M data/Aspergillus_nidulans/21.jf
226M data/Aspergillus_nidulans
33M data/Aspergillus_niger/Aspergillus_niger.fasta
4.0K data/Aspergillus_niger/21.jf.timming
226M data/Aspergillus_niger/21.jf
259M data/Aspergillus_niger
36M data/Aspergillus_oryzae/Aspergillus_oryzae.fasta
4.0K data/Aspergillus_oryzae/21.jf.timming
246M data/Aspergillus_oryzae/21.jf
282M data/Aspergillus_oryzae
15M data/Candida_dubliniensis/Candida_dubliniensis.fasta
4.0K data/Candida_dubliniensis/21.jf.timming
93M data/Candida_dubliniensis/21.jf
108M data/Candida_dubliniensis
12M data/Candida_glabrata/Candida_glabrata.fasta
4.0K data/Candida_glabrata/21.jf.timming
81M data/Candida_glabrata/21.jf
93M data/Candida_glabrata
18M data/Cryptococcus_gattii/Cryptococcus_gattii.fasta
4.0K data/Cryptococcus_gattii/21.jf.timming
118M data/Cryptococcus_gattii/21.jf
136M data/Cryptococcus_gattii
20M data/Cryptococcus_neoformans/Cryptococcus_neoformans.fasta
4.0K data/Cryptococcus_neoformans/21.jf.timming
122M data/Cryptococcus_neoformans/21.jf
141M data/Cryptococcus_neoformans
11M data/Kluyveromyces_lactis/Kluyveromyces_lactis.fasta
4.0K data/Kluyveromyces_lactis/21.jf.timming
71M data/Kluyveromyces_lactis/21.jf
82M data/Kluyveromyces_lactis
40M data/Neurospora_crassa/Neurospora_crassa.fasta
4.0K data/Neurospora_crassa/21.jf.timming
267M data/Neurospora_crassa/21.jf
307M data/Neurospora_crassa
12M data/Saccharomyces_cerevisiae/Saccharomyces_cerevisiae.fasta
4.0K data/Saccharomyces_cerevisiae/21.jf.timming
77M data/Saccharomyces_cerevisiae/21.jf
89M data/Saccharomyces_cerevisiae
13M data/Schizosaccharomyces_pombe/Schizosaccharomyces_pombe.fasta
4.0K data/Schizosaccharomyces_pombe/21.jf.timming
82M data/Schizosaccharomyces_pombe/21.jf
94M data/Schizosaccharomyces_pombe
20M data/Yarrowia_lipolytica/Yarrowia_lipolytica.fasta
4.0K data/Yarrowia_lipolytica/21.jf.timming
134M data/Yarrowia_lipolytica/21.jf
154M data/Yarrowia_lipolytica
9.5M data/Zygosaccharomyces_rouxii/Zygosaccharomyces_rouxii.fasta
4.0K data/Zygosaccharomyces_rouxii/21.jf.timming
65M data/Zygosaccharomyces_rouxii/21.jf
74M data/Zygosaccharomyces_rouxii
2.3G data
The output:
$ ls test/out/
Makefile
$ ls test/out/test/
total 1.2M
12K Makefile
28K test_0001_0001.cnm
16K test_0001_0001.json
4.0K test_0001_0001.json.count.csv
4.0K test_0001_0001.json.csv
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity.matrix
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity.nj
72K test_0001_0001.json.no_scale.jaccard_dissimilarity.nj.png
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity.nj.tree
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.matrix
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.nj
76K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.nj.png
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.nj.tree
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.upgma
76K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.upgma.png
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity_sqrt.upgma.tree
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity.upgma
76K test_0001_0001.json.no_scale.jaccard_dissimilarity.upgma.png
4.0K test_0001_0001.json.no_scale.jaccard_dissimilarity.upgma.tree
0 test_0001_0001.json.pngok
416K test_0001_0001.log
0 test_0001_0001.ok
4.0K test.all.count.csv
8.0K test.all.csv
0 test.cnm
0 test.json
4.0K test.json.count.csv
4.0K test.json.csv
4.0K test.json.no_scale.jaccard_dissimilarity.matrix
4.0K test.json.no_scale.jaccard_dissimilarity.nj
72K test.json.no_scale.jaccard_dissimilarity.nj.png
4.0K test.json.no_scale.jaccard_dissimilarity.nj.tree
4.0K test.json.no_scale.jaccard_dissimilarity_sqrt.matrix
4.0K test.json.no_scale.jaccard_dissimilarity_sqrt.nj
72K test.json.no_scale.jaccard_dissimilarity_sqrt.nj.png
4.0K test.json.no_scale.jaccard_dissimilarity_sqrt.nj.tree
4.0K test.json.no_scale.jaccard_dissimilarity_sqrt.upgma
76K test.json.no_scale.jaccard_dissimilarity_sqrt.upgma.png
4.0K test.json.no_scale.jaccard_dissimilarity_sqrt.upgma.tree
4.0K test.json.no_scale.jaccard_dissimilarity.upgma
72K test.json.no_scale.jaccard_dissimilarity.upgma.png
4.0K test.json.no_scale.jaccard_dissimilarity.upgma.tree
0 test.json.pngok
4.0K test.log
0 test.ok
The phylogenetic trees:
$ cat test.json.no_scale.jaccard_dissimilarity.nj.tree
/-Cryptococcus neoformans var JEC21 uid10698
/edge.0--|
| \-Cryptococcus gattii WM276
|
/edge.4--| /-Aspergillus niger CBS 513 88 uid19263
| | /edge.1--|
| | /edge.2--| \-Aspergillus oryzae RIB40 uid28175
| | | |
| \edge.3--| \-Aspergillus fumigatus uid14003
| |
| \-Aspergillus nidulans FGSC A4 uid13961
|
-root----| /-Neurospora crassa uid132
|-edge.5--|
| \-Yarrowia lipolytica CLIB122 uid12414
|
| /-Candida dubliniensis CD36 uid38659
| /edge.9--|
| | | /-Zygosaccharomyces rouxii CBS 732 uid39573
| | \edge.8--|
| | | /-Kluyveromyces lactis NRRL Y-1140 uid12377
\edge.10-| \edge.7--|
| | /-Candida glabrata CBS138 uid12376
| \edge.6--|
| \-Saccharomyces cerevisiae uid128
|
\-Schizosaccharomyces pombe uid127
Newick tree
$ cat test.json.no_scale.jaccard_dissimilarity.nj
(((Cryptococcus_neoformans_var_JEC21_uid10698:0.0178604557174,Cryptococcus_gattii_WM276:0.0173134981567):0.4993077284,(((Aspergillus_niger_CBS_513_88_uid19263:0.345930782661,Aspergillus_oryzae_RIB40_uid28175:0.346370249728):0.034782079948,Aspergillus_fumigatus_uid14003:0.385379378235):0.0393350255391,Aspergillus_nidulans_FGSC_A4_uid13961:0.426129781102):0.0548021380182):0.0111478680149,('Neurospora crassa uid132':0.432396815528,Yarrowia_lipolytica_CLIB122_uid12414:0.44897381579):0.0177549831691,((Candida_dubliniensis_CD36_uid38659:0.416702677849,(Zygosaccharomyces_rouxii_CBS_732_uid39573:0.408443601479,(Kluyveromyces_lactis_NRRL_Y-1140_uid12377:0.395501824207,(Candida_glabrata_CBS138_uid12376:0.383440146903,Saccharomyces_cerevisiae_uid128:0.373946775161):0.0135771064445):0.0234388374394):0.0488771035835):0.0164746506052,Schizosaccharomyces_pombe_uid127:0.469881795743):0.013057881288);
Image:
