Commit 2439efc1 authored by Carine Rey's avatar Carine Rey
Browse files

change python_basics docker version

parent 07315f01
......@@ -22,6 +22,6 @@ RUN apt-get update && \
RUN pip install --upgrade pip
RUN pip install ete3==3.0.0b35
RUN pip install scipy==0.19.1
RUN pip install scipy==1.1.0
RUN pip install biopython==1.72
......@@ -4,7 +4,7 @@ set -e
IMAGE_NAME=python_basics
DOCKERFILE_DIR=.
TAG=07172018
TAG=07182018
REPO=carinerey/$IMAGE_NAME:$TAG
docker build -t $REPO -f ./Dockerfile $DOCKERFILE_DIR
......
......@@ -42,7 +42,7 @@ type dataset_res = {
}
let merge_results ~res_by_tools : text_file workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07172018" () in
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07182018" () in
let command = List.map res_by_tools ~f:(fun res ->
let w = match res with
| `Pcoc d -> Pcoc.results d
......@@ -97,7 +97,7 @@ let plot_merge_results ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~t
| `Topological_LG _ -> "Topological_LG08"
| `Topological_WAG _ -> "Topological_WAG01"
| `Tdg09 _ -> "Tdg09_1-FDR,Tdg09_prob_post"
| `Multinomial _ -> ""
| `Multinomial _ -> "Mutinomial_LRT"
in
string opt
) |> seq ~sep:","
......@@ -114,7 +114,7 @@ let plot_merge_results ~plot_all_sites ~(res_by_tools:result list) ~tree ~faa ~t
| `Topological_LG _ -> "Topological_LG08:0.9"
| `Topological_WAG _ -> "Topological_WAG01:0.9"
| `Tdg09 _ -> "Tdg09_1-FDR:0.9,Tdg09_prob_post:0.9"
| `Multinomial _ -> ""
| `Multinomial _ -> "Mutinomial_LRT:0.9"
in
string opt
) |> seq ~sep:","
......
......@@ -5,7 +5,7 @@ open Bistro_bioinfo.Std
open File_formats
let multinomial ~(tree_id:_ workflow) ~(tree_sc:_ workflow) ~(faa:aminoacid_fasta workflow) : [`multinomial] directory workflow =
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07172018" () in
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07182018" () in
workflow ~descr:("calc_multinomial") [
mkdir_p dest;
cmd "python" ~env [
......
......@@ -132,13 +132,15 @@ if args.topological_LG :
if args.topological_WAG :
df_topological_WAG = pd.read_csv(args.topological_WAG, sep="\t")
df_topological_WAG.rename(columns={'Topological': 'Topological_WAG01'}, inplace=True)
if args.tdg09 :
df_tdg09 = pd.read_csv(args.tdg09, sep="\t")
if args.multinomial :
df_multinomial = pd.read_csv(args.multinomial, sep="\t")
df_multinomial.rename(columns={'LRT': 'Mutinomial_LRT',
'LikelihoodRatio' :"Multinomial_LikelihoodRatio"}, inplace=True)
df_list = [df for df in [df_pcoc, df_pcoc_gamma, df_pcoc_C60,
df_diffsel, df_diffsel_bis,
......
......@@ -3,7 +3,7 @@ open Bistro.EDSL
open Bistro.Std
open File_formats
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07172018" ()
let env = docker_image ~account:"carinerey" ~name:"python_basics" ~tag:"07182018" ()
let prepare tree =
workflow ~descr:"utils.parse_input_tree" [
......
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