Merge branch 'freq_matrix_overwritten' into 'master'

Added installer for virtual env

See merge request !2

phages/scripts/00_create_py_env.sh

+#!/bin/bash
+
+## VARIABLES
+
+## Directory containing the virtual environment
+py_env_dir=~/envs/coev
+
+## url for the desired python3 executable
+py_version=$(readlink $(command -v python3))
+
+echo 'Environment to be installed in: ' $py_env_dir
+echo 'Version of python to be used: ' $py_version
+
+
+## SCRIPT
+
+mkdir -p  $py_env_dir
+virtualenv  -p $py_version  $py_env_dir
+
+
+## INSTALL  PACKAGES
+
+# Activate environment
+source  ${py_env_dir}/bin/activate
+
+# Update pip if necessary
+pip install --upgrade pip
+
+## 
+pip install  -r requirements_py-env.txt
+# pip  install  biopython  pandas   matplotlib  multiqc  pyvcf
+
+
+deactivate

phages/scripts/01_quality_check.sh

@@ -2,11 +2,14 @@
 
 
 ## PATH TO WORKING DIRECTORY
-path=/home/enrique/work/Gandon/coevolution/phages/
+path=$1
+#path=/home/enrique/work/Gandon/coevolution/phages/
+
 
 
 ## START ENVIRONMENT TO EXECUTE MULTIQC
-source /home/enrique/envs/biopython/bin/activate
+
+source ~/envs/coev/bin/activate
 
 
 ## SEPARATE THE FILES BY NAME 

phages/scripts/07_2_test.py

@@ -16,7 +16,8 @@ def run_on_multiple_files(path_to_vcfs, outpath, list_files, list_headers, group
 
 
 
-ctrl_file = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/Other_seq/TO-WT_S83.vcf'
+#ctrl_file = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/Other_seq/TO-WT_S83.vcf'
+ctrl_file='/mnt/alpha_raid/work/Gandon/coevolution/phages/steps/snpcalling/Other_seq/TO-WT_S83.vcf'
 
 control = ImportControl2()
 
@@ -25,7 +26,7 @@ control.load_vcf(ctrl_file)
 
 
 
-path_to_vcfs = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/W_seq/'
+path_to_vcfs = '/mnt/alpha_raid/work/Gandon/coevolution/phages/steps/snpcalling/W_seq/'
 
 outpath = '/mnt/alpha_raid/work/Gandon/coevolution/phages/plots/freq_heatmap/W_seq/'
 

phages/scripts/requirements_py-env.txt

+biopython==1.76
+certifi==2019.11.28
+chardet==3.0.4
+Click==7.0
+coloredlogs==10.0
+colormath==3.0.0
+cycler==0.10.0
+decorator==4.4.1
+future==0.18.2
+humanfriendly==4.18
+idna==2.8
+Jinja2==2.10.3
+kiwisolver==1.1.0
+lzstring==1.0.4
+Markdown==3.1.1
+MarkupSafe==1.1.1
+matplotlib==2.2.4
+multiqc==1.8
+networkx==2.2
+numpy==1.18.1
+pandas==0.24.2
+pyparsing==2.4.6
+python-dateutil==2.8.1
+pytz==2019.3
+PyVCF==0.6.8
+PyYAML==5.3
+requests==2.22.0
+simplejson==3.17.0
+six==1.13.0
+spectra==0.0.11
+urllib3==1.25.7