Skip to content

Commit

Permalink
merge branch dev : add FROGSSTAT tools
Browse files Browse the repository at this point in the history
  • Loading branch information
mariabernard committed Jun 28, 2017
2 parents 4278388 + 5cd6911 commit e3bd3c6
Show file tree
Hide file tree
Showing 84 changed files with 3,973 additions and 5 deletions.
46 changes: 42 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,7 @@
PATH and 'lib' must be accessible in the PYTHONPATH.

### 3. Install dependencies
Dependencies must be accessible in the PATH or added in
<FROGS_PATH>/libexec.
Dependencies must be accessible in the PATH or added in <FROGS_PATH>/libexec.

python interpreter
Version: 2.7
Expand Down Expand Up @@ -136,13 +135,13 @@

RDPClassifier
Version: -
Name as: classifier.jar
Named as: classifier.jar
Tools: affiliation_OTU
Download: https://github.com/rdpstaff/RDPTools

taskset
Version: util-linux-ng 2.17.2
Name as: taskset
Named as: taskset
Tools: affiliation_OTU
Install: sudo apt-get install util-linux
OR
Expand All @@ -166,6 +165,45 @@
Tools: tree
Download: http://www.microbesonline.org/fasttree/#Install

RScript
Version : >= 3.3.0
Named as : RScript
Tools : all FROGS_Phyloseq and FROGS_DESeq
Download : https://cran.r-project.org/

Rmarkdown R package
Version : depending on your R version
Tools : all FROGS_Phyloseq and FROGS_DESeq
Install in R session : # https://cran.r-project.org/web/packages/rmarkdown/index.html
install.packages("rmarkdown")

Pandoc
Version : >= 1.12.3
Named as : pandoc
Tools : all FROGS_Phyloseq and FROGS_DESeq
Download/Installation : # http://pandoc.org/installing.html#linux or simply soft-link pandoc binary from RStudio path (if you have Rstudio installed)

Phyloseq R package
Version : depending on your R version
Tools : all FROGS_Phyloseq
Installation in R session : # https://joey711.github.io/phyloseq/install.html
source("https://bioconductor.org/biocLite.R") ; biocLite("phyloseq")
Test in R session : library(phyloseq)

Plotly R package
Version : depending on your R version
Tools : FROGS_Phyloseq_composition and FROGS_Phyloseq_structure
Installation in R session : # https://plot.ly/r/getting-started/
install.packages("plotly")
Test in R session : library(plotly)

GridExtra R package
Version : depending on your R version
Tools : FROGS_Phyloseq_Beta_Diversity, FROGS_Phyloseq_Sample_Clustering, FROGS_Phyloseq_composition and FROGS_Phyloseq_structure
Installation in R session : # https://cran.r-project.org/web/packages/gridExtra/index.html
install.packages("gridExtra")
Test in R session : library(gridExtra)

### 4. Check intallation
To check your installation you can type:
cd <FROGS_PATH>/test
Expand Down
7 changes: 7 additions & 0 deletions RELEASES_NOTES.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,13 @@
# v2.0.0 [DEV]
### Tools added :
* Tree : perform phylogenetic tree reconstruction based on Pynast or Mafft and Fasttree
* FROGS Phyloseq Import Data : import data from 3 files: biomfile, samplefile, treefile into a phyloseq R object.
* FROGS Phyloseq Composition Visualization with bar plot and composition plot
* FROGS Phyloseq Alpha Diversity with richness plot
* FROGS Phyloseq Beta Diversity distance matrix
* FROGS Phyloseq Structure
* FROGS Phyloseq Clustering
* FROGS Phyloseq Manova

### Bugs fixes:
* Preprocess : min overlap at least equal to 1
Expand Down
1 change: 1 addition & 0 deletions app/r_alpha_diversity.Rmd
1 change: 1 addition & 0 deletions app/r_alpha_diversity.py
1 change: 1 addition & 0 deletions app/r_alpha_diversity.xml
1 change: 1 addition & 0 deletions app/r_beta_diversity.Rmd
1 change: 1 addition & 0 deletions app/r_beta_diversity.py
1 change: 1 addition & 0 deletions app/r_beta_diversity.xml
1 change: 1 addition & 0 deletions app/r_clustering.Rmd
1 change: 1 addition & 0 deletions app/r_clustering.py
1 change: 1 addition & 0 deletions app/r_clustering.xml
1 change: 1 addition & 0 deletions app/r_composition.Rmd
1 change: 1 addition & 0 deletions app/r_composition.py
1 change: 1 addition & 0 deletions app/r_composition.xml
1 change: 1 addition & 0 deletions app/r_import_data.Rmd
1 change: 1 addition & 0 deletions app/r_import_data.py
1 change: 1 addition & 0 deletions app/r_import_data.xml
1 change: 1 addition & 0 deletions app/r_manova.Rmd
1 change: 1 addition & 0 deletions app/r_manova.py
1 change: 1 addition & 0 deletions app/r_manova.xml
1 change: 1 addition & 0 deletions app/r_structure.Rmd
1 change: 1 addition & 0 deletions app/r_structure.py
1 change: 1 addition & 0 deletions app/r_structure.xml
Binary file added img/biomfile.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file removed img/frogs_tree_view_phyloviz.png
Binary file not shown.
File renamed without changes
Binary file added img/phyloseq_alpha_diversity_table.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_bar_plot.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_beta_diversity.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_beta_diversity_matrix.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_clustering_ward.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_composition_plot.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_import_data_html.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_manova.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_plot_heatmap_red.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_plot_richness.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_plot_richness_box.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_plot_sample_ellipse.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_rarefaction_curves.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added img/phyloseq_samplefile.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
7 changes: 7 additions & 0 deletions tools/biom_to_tsv/biom_to_tsv.py
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ def __init__( self, out_tsv, in_biom, in_fasta=None ):

# Check the metadata
biom = BiomIO.from_json( in_biom )
obs = biom.rows[0]
conversion_tags = ""
if biom.has_observation_metadata( 'rdp_taxonomy' ) and biom.has_observation_metadata( 'rdp_bootstrap' ):
conversion_tags += "'@rdp_tax_and_bootstrap' "
Expand All @@ -76,6 +77,12 @@ def __init__( self, out_tsv, in_biom, in_fasta=None ):
conversion_tags += "'seed_id' "
if in_fasta is not None:
conversion_tags += "'@seed_sequence' "

frogs_metadata = ["rdp_taxonomy", "rdp_bootstrap","blast_taxonomy","blast_affiliations","seed_id"]
for metadata in biom.get_observation_metadata(obs["id"]):
if metadata not in frogs_metadata :
conversion_tags += "'"+metadata+"' "

conversion_tags += "'@observation_name' '@observation_sum' '@sample_count'"

# Set command
Expand Down
Binary file added tools/phylo_alpha_diversity/data/data.Rdata
Binary file not shown.
Loading

0 comments on commit e3bd3c6

Please sign in to comment.