Use argparse instead of optparse for CL handling in R. Update Makefil…

…e, README, anaconda environment and comput_PI.R accordingly.

Makefile

@@ -145,16 +145,16 @@ wgs_qc : $(WGS)/mapped $(WGS)/raw
 wgs_wild : $(CORRESP) $(SIZES) $(WGS)/variant/hap.wild.matrix
  # Compute PI diversity in sliding windows
  Rscript src/wgs_wild/compute_PI.R \
- -i $(WGS)/variant/hap.wild.matrix.txt \
- -o $(WGS)/stats/win_w100_t10_PI.tsv \
- -m 'window' \
+ --in $(WGS)/variant/hap.wild.matrix.txt \
+ --out $(WGS)/stats/win_w100_t10_PI.tsv \
+ --mode 'window' \
  --step_size 10 \
  --win_size 100
  # Compute PI diversity per site
  Rscript src/wgs_wild/compute_PI.R
- -i $(WGS)/variant/hap.wild.matrix.txt \
- -o $(WGS)/stats/sites_PI.tsv \
- -m 'site'
+ --in $(WGS)/variant/hap.wild.matrix.txt \
+ --out $(WGS)/stats/sites_PI.tsv \
+ --mode 'site'
 
 ####################
 #### MISC RULES ####

README.md

@@ -59,13 +59,13 @@ These dependencies are required to run the main analysis. This include the RADse
 * [VCFtools 0.1.15](https://vcftools.github.io/)
 * [BEDtools 2.26](https://bedtools.readthedocs.io/)
 * [Trimmomatic 0.36](https://usadellab.org/cms/?page=trimmomatic)
-* [R 3.4.1](https://www.r-project.org/)
- + [tidyverse 1.1.1](https://www.tidyverse.org)
+* [R 3.4.3](https://www.r-project.org/)
+ + [tidyverse 1.2.1](https://www.tidyverse.org)
  + [zoo 1.8.0](https://cran.r-project.org/web/packages/zoo/index.html)
- + [Rcpp 0.12.11](https://cran.r-project.org/web/packages/Rcpp/)
+ + [Rcpp 0.12.14](https://cran.r-project.org/web/packages/Rcpp/)
  + [RcppRoll 0.2.2](https://cran.r-project.org/web/packages/RcppRoll/)
  + [viridis 0.4.0](https://cran.r-project.org/web/packages/viridis/vignettes/intro-to-viridis.html)
- + [optparse 1.6.0](https://cran.r-project.org/web/packages/optparse)
+ + [argparse 1.1.0](https://cran.r-project.org/web/packages/argparse/index.html)
  + [gridExtra 2.3](https://cran.r-project.org/web/packages/gridExtra/index.html)
 * [Python 2.7.x](https://www.python.org/)
  + [numpy 1.11](https://www.numpy.org/)

docs/csd_env_conda.yml

@@ -1,130 +1,169 @@
 name: csd_env
 channels:
- - conda-forge
+ - r
  - defaults
 dependencies:
- - ca-certificates=2018.4.16=0
- - certifi=2018.4.16=py27_0
- - icu=58.2=hfc679d8_0
- - libpng=1.6.28=2
- - libtiff=4.0.7=1
- - openssl=1.0.2o=h470a237_1
- - pyqt=4.11.4=py27_3
- - r-base=3.4.1=2
- - r-getopt=1.20.2=r3.4.1_0
- - r-optparse=1.6.0=r341_0
- - r-rcpproll=0.2.2=r3.4.1_0
- - sip=4.18=py27_1
- - _r-mutex=1.0.0=mro_2
+ - binutils_impl_linux-64=2.28.1=had2808c_3
+ - binutils_linux-64=7.2.0=had2808c_27
  - biopython=1.72=py27h04863e7_0
  - blas=1.0=mkl
+ - bwidget=1.9.11=0
  - bzip2=1.0.6=h14c3975_5
- - cairo=1.14.8=0
+ - ca-certificates=2018.03.07=0
+ - cairo=1.14.12=h8948797_3
+ - certifi=2018.4.16=py27_0
  - curl=7.61.0=h84994c4_0
  - cycler=0.10.0=py27_0
- - dbus=1.10.20=0
+ - dbus=1.13.2=h714fa37_1
  - expat=2.2.5=he0dffb1_0
- - fontconfig=2.12.1=3
- - freetype=2.5.5=2
- - glib=2.50.2=1
+ - fontconfig=2.13.0=h9420a91_0
+ - freetype=2.9.1=h8a8886c_0
+ - fribidi=1.0.4=h14c3975_0
+ - gcc_impl_linux-64=7.2.0=habb00fd_3
+ - gcc_linux-64=7.2.0=h550dcbe_27
+ - gfortran_impl_linux-64=7.2.0=hdf63c60_3
+ - gfortran_linux-64=7.2.0=h550dcbe_27
+ - glib=2.56.1=h000015b_0
+ - graphite2=1.3.11=h16798f4_2
  - gsl=2.4=h14c3975_4
- - gst-plugins-base=1.8.0=0
- - gstreamer=1.8.0=0
- - harfbuzz=0.9.39=2
+ - gst-plugins-base=1.14.0=hbbd80ab_1
+ - gstreamer=1.14.0=hb453b48_1
+ - gxx_impl_linux-64=7.2.0=hdf63c60_3
+ - gxx_linux-64=7.2.0=h550dcbe_27
+ - harfbuzz=1.8.4=hec2c2bc_0
+ - icu=58.2=h9c2bf20_1
  - intel-openmp=2018.0.3=0
  - jpeg=9b=h024ee3a_2
+ - krb5=1.14.2=hcdc1b81_6
  - libcurl=7.61.0=h1ad7b7a_0
+ - libedit=3.1=heed3624_0
  - libffi=3.2.1=hd88cf55_4
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=7.2.0=hdf63c60_3
  - libgfortran-ng=7.2.0=hdf63c60_3
  - libiconv=1.14=0
+ - libopenblas=0.2.20=h9ac9557_7
+ - libpng=1.6.34=hb9fc6fc_0
  - libssh2=1.8.0=h9cfc8f7_4
  - libstdcxx-ng=7.2.0=hdf63c60_3
+ - libtiff=4.0.9=he85c1e1_1
+ - libuuid=1.0.3=h1bed415_2
  - libxcb=1.13=h1bed415_1
- - libxml2=2.9.4=0
- - matplotlib=1.5.1=np111py27_0
+ - libxml2=2.9.8=h26e45fe_1
  - mkl=2018.0.3=1
- - ncurses=5.9=10
+ - ncurses=6.0=h9df7e31_2
  - numpy=1.11.3=py27h1b885b7_9
  - numpy-base=1.11.3=py27h3dfced4_9
+ - openssl=1.0.2o=h20670df_0
  - pandas=0.19.2=np111py27_1
- - pango=1.40.3=1
- - pcre=8.39=1
+ - pango=1.42.2=h8589676_0
+ - pcre=8.42=h439df22_0
  - pip=10.0.1=py27_0
  - pixman=0.34.0=hceecf20_3
  - pycairo=1.13.3=py27hea6d626_0
  - pyparsing=2.2.0=py27_1
- - python=2.7.13=0
+ - pyqt=5.9.2=py27h22d08a2_0
+ - python=2.7.15=h1571d57_0
  - python-dateutil=2.7.3=py27_0
  - pytz=2018.5=py27_0
- - qt=4.8.7=4
- - r-assertthat=0.2.0=r3.4.1_0
- - r-bh=1.62.0_1=r3.4.1_0
- - r-bindr=0.1=r3.4.1_0
- - r-bindrcpp=0.2=r3.4.1_0
- - r-broom=0.4.2=r3.4.1_0
- - r-cellranger=1.1.0=r3.4.1_0
- - r-colorspace=1.3_2=r3.4.1_0
- - r-curl=2.6=r3.4.1_0
- - r-dichromat=2.0_0=r3.4.1_2
- - r-digest=0.6.12=r3.4.1_0
- - r-dplyr=0.7.0=r3.4.1_0
- - r-forcats=0.2.0=r3.4.1_0
- - r-foreign=0.8_68=r3.4.1_0
- - r-ggplot2=2.2.1=r3.4.1_0
- - r-glue=1.1.1=r3.4.1_0
- - r-gridextra=2.2.1=r3.4.1_0
- - r-gtable=0.2.0=r3.4.1_0
- - r-haven=1.0.0=r3.4.1_0
- - r-hms=0.3=r3.4.1_0
- - r-httr=1.2.1=r3.4.1_0
- - r-jsonlite=1.5=r3.4.1_0
- - r-labeling=0.3=r3.4.1_2
- - r-lattice=0.20_35=r3.4.1_0
- - r-lazyeval=0.2.0=r3.4.1_0
- - r-lubridate=1.6.0=r3.4.1_0
- - r-magrittr=1.5=r3.4.1_2
- - r-mass=7.3_47=r3.4.1_0
- - r-mime=0.5=r3.4.1_0
- - r-mnormt=1.5_5=r3.4.1_0
- - r-modelr=0.1.0=r3.4.1_0
- - r-munsell=0.4.3=r3.4.1_0
- - r-nlme=3.1_131=r3.4.1_0
- - r-openssl=0.9.6=r3.4.1_0
- - r-pkgconfig=2.0.1=r3.4.1_0
- - r-plogr=0.1_1=r3.4.1_0
- - r-plyr=1.8.4=r3.4.1_0
- - r-psych=1.7.5=r3.4.1_0
- - r-purrr=0.2.2.2=r3.4.1_0
- - r-r6=2.2.1=r3.4.1_0
- - r-rcolorbrewer=1.1_2=r3.4.1_3
- - r-rcpp=0.12.11=r3.4.1_0
- - r-readr=1.1.1=r3.4.1_0
- - r-readxl=1.0.0=r3.4.1_0
- - r-rematch=1.0.1=r3.4.1_0
- - r-reshape2=1.4.2=r3.4.1_0
- - r-rlang=0.1.1=r3.4.1_0
- - r-rvest=0.3.2=r3.4.1_0
- - r-scales=0.4.1=r3.4.1_0
- - r-selectr=0.3_1=r3.4.1_0
- - r-stringi=1.1.5=r3.4.1_0
- - r-stringr=1.2.0=r3.4.1_0
- - r-tibble=1.3.3=r3.4.1_0
- - r-tidyr=0.6.3=r3.4.1_0
- - r-tidyverse=1.1.1=r3.4.1_0
- - r-viridis=0.4.0=r3.4.1_0
- - r-viridislite=0.2.0=r3.4.1_0
- - r-xml2=1.1.1=r3.4.1_0
- - r-zoo=1.8_0=r3.4.1_0
- - readline=6.2=2
+ - qt=5.9.6=h52aff34_0
+ - readline=7.0=ha6073c6_4
  - setuptools=39.2.0=py27_0
+ - sip=4.19.8=py27hf484d3e_0
  - six=1.11.0=py27_1
- - sqlite=3.13.0=0
- - tk=8.5.18=0
+ - sqlite=3.23.1=he433501_0
+ - tk=8.6.7=hc745277_3
+ - tktable=2.10=h14c3975_0
  - wheel=0.31.1=py27_0
  - xz=5.2.4=h14c3975_4
  - zlib=1.2.11=ha838bed_2
+ - _r-mutex=1.0.0=anacondar_1
+ - r-argparse=1.1.0=r343h889e2dd_0
+ - r-assertthat=0.2.0=r343h889e2dd_0
+ - r-backports=1.1.2=r343h086d26f_0
+ - r-base=3.4.3=h290ecf8_1
+ - r-base64enc=0.1_3=r343h086d26f_4
+ - r-bh=1.65.0_1=r343h889e2dd_0
+ - r-bindr=0.1=r343h889e2dd_0
+ - r-bindrcpp=0.2=r343h599a50d_0
+ - r-broom=0.4.3=r343h889e2dd_0
+ - r-callr=1.0.0=r343h889e2dd_0
+ - r-cellranger=1.1.0=r343h889e2dd_0
+ - r-cli=1.0.0=r343h889e2dd_0
+ - r-clipr=0.4.0=r343h889e2dd_0
+ - r-colorspace=1.3_2=r343h086d26f_0
+ - r-crayon=1.3.4=r343h889e2dd_0
+ - r-curl=3.1=r343h086d26f_0
+ - r-dbi=0.7=r343h889e2dd_0
+ - r-dbplyr=1.1.0=r343h889e2dd_0
+ - r-dichromat=2.0_0=r343h889e2dd_4
+ - r-digest=0.6.13=r343h086d26f_0
+ - r-dplyr=0.7.4=r343h599a50d_0
+ - r-evaluate=0.10.1=r343h889e2dd_0
+ - r-findpython=1.0.3=r343h889e2dd_0
+ - r-forcats=0.2.0=r343h889e2dd_0
+ - r-foreign=0.8_69=r343h086d26f_0
+ - r-getopt=1.20.1=r343h889e2dd_0
+ - r-ggplot2=2.2.1=r343h889e2dd_0
+ - r-glue=1.2.0=r343h086d26f_0
+ - r-gridextra=2.3=r343h889e2dd_0
+ - r-gtable=0.2.0=r343h889e2dd_0
+ - r-haven=1.1.0=r343h599a50d_0
+ - r-highr=0.6=r343h889e2dd_0
+ - r-hms=0.4.0=r343h889e2dd_0
+ - r-htmltools=0.3.6=r343h599a50d_0
+ - r-httr=1.3.1=r343h889e2dd_0
+ - r-jsonlite=1.5=r343h086d26f_0
+ - r-knitr=1.18=r343h889e2dd_0
+ - r-labeling=0.3=r343h889e2dd_4
+ - r-lattice=0.20_35=r343h086d26f_0
+ - r-lazyeval=0.2.1=r343h086d26f_0
+ - r-lubridate=1.7.1=r343h599a50d_0
+ - r-magrittr=1.5=r343h889e2dd_4
+ - r-markdown=0.8=r343h086d26f_0
+ - r-mass=7.3_48=r343h086d26f_0
+ - r-mime=0.5=r343h086d26f_0
+ - r-mnormt=1.5_5=r343h4829c52_0
+ - r-modelr=0.1.1=r343h889e2dd_0
+ - r-munsell=0.4.3=r343h889e2dd_0
+ - r-nlme=3.1_131=r343h4829c52_0
+ - r-openssl=0.9.9=r343h086d26f_0
+ - r-pillar=1.0.1=r343h889e2dd_0
+ - r-pkgconfig=2.0.1=r343h889e2dd_0
+ - r-plogr=0.1_1=r343h889e2dd_0
+ - r-plyr=1.8.4=r343h599a50d_0
+ - r-proto=1.0.0=r343h889e2dd_0
+ - r-psych=1.7.8=r343h889e2dd_0
+ - r-purrr=0.2.4=r343h086d26f_0
+ - r-r6=2.2.2=r343h889e2dd_0
+ - r-rcolorbrewer=1.1_2=r343h889e2dd_0
+ - r-rcpp=0.12.14=r343h599a50d_0
+ - r-rcpproll=0.2.2=r343h599a50d_0
+ - r-readr=1.1.1=r343h599a50d_0
+ - r-readxl=1.0.0=r343h599a50d_0
+ - r-rematch=1.0.1=r343h889e2dd_0
+ - r-reprex=0.1.1=r343h889e2dd_0
+ - r-reshape2=1.4.3=r343h599a50d_0
+ - r-rlang=0.1.6=r343h086d26f_0
+ - r-rmarkdown=1.8=r343h889e2dd_0
+ - r-rprojroot=1.3_1=r343h889e2dd_0
+ - r-rstudioapi=0.7=r343h889e2dd_0
+ - r-rvest=0.3.2=r343h889e2dd_0
+ - r-scales=0.5.0=r343h599a50d_0
+ - r-selectr=0.3_1=r343h889e2dd_0
+ - r-stringi=1.1.6=r343h599a50d_0
+ - r-stringr=1.2.0=r343h889e2dd_0
+ - r-tibble=1.4.1=r343h086d26f_0
+ - r-tidyr=0.7.2=r343h599a50d_0
+ - r-tidyselect=0.2.3=r343h599a50d_0
+ - r-tidyverse=1.2.1=r343h889e2dd_0
+ - r-utf8=1.1.2=r343h086d26f_0
+ - r-viridis=0.4.0=r343h889e2dd_0
+ - r-viridislite=0.2.0=r343h889e2dd_0
+ - r-whisker=0.3_2=r343h889e2dd_4
+ - r-xml2=1.1.1=r343h599a50d_0
+ - r-yaml=2.1.16=r343h086d26f_0
+ - r-zoo=1.8_0=r343h086d26f_0
  - pip:
  - backports.shutil-get-terminal-size==1.0.0
  - enum34==1.1.6
@@ -143,3 +182,4 @@ dependencies:
  - simplegeneric==0.8.1
  - traitlets==4.3.2
  - wcwidth==0.1.7
+prefix: /home/cyril/Software/anaconda3/envs/csd_env