https://bioinformaticsonline.com/snippets/owner/rahul?offset=20 https://bioinformaticsonline.com/snippets/view/40805/bash-command-to-install-gatk-bedtools-and-snpeff Sat, 01 Feb 2020 02:29:09 -0600 https://bioinformaticsonline.com/snippets/view/40805/bash-command-to-install-gatk-bedtools-and-snpeff (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - gatk The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2019.11.28 | py38_0 156 KB gatk-3.8 | 7 8 KB bioconda pip-20.0.2 | py38_1 1.9 MB python-3.8.1 | h0371630_1 57.8 MB r-assertthat-0.2.1 | r36h6115d3f_0 74 KB r-bitops-1.0_6 | r36h96ca727_4 34 KB r-catools-1.17.1.2 | r36h29659fb_0 223 KB r-cli-1.1.0 | r36h6115d3f_0 189 KB r-colorspace-1.4_1 | r36h96ca727_0 2.5 MB r-crayon-1.3.4 | r36h6115d3f_0 757 KB r-dichromat-2.0_0 | r36h6115d3f_4 163 KB r-digest-0.6.18 | r36h96ca727_0 155 KB r-fansi-0.4.0 | r36h96ca727_0 193 KB r-gdata-2.18.0 | r36h6115d3f_0 1.1 MB r-ggplot2-3.1.1 | r36h6115d3f_0 3.6 MB r-glue-1.3.1 | r36h96ca727_0 165 KB r-gplots-3.0.1.1 | r36h6115d3f_0 699 KB r-gsalib-2.1 | r36h6115d3f_0 31 KB r-gtable-0.3.0 | r36h6115d3f_0 425 KB r-gtools-3.8.1 | r36h96ca727_0 325 KB r-kernsmooth-2.23_15 | r36ha65eedd_4 102 KB r-labeling-0.3 | r36h6115d3f_4 71 KB r-lattice-0.20_38 | r36h96ca727_0 1.1 MB r-lazyeval-0.2.2 | r36h96ca727_0 164 KB r-magrittr-1.5 | r36h6115d3f_4 173 KB r-mass-7.3_51.3 | r36h96ca727_0 1.1 MB r-matrix-1.2_17 | r36h96ca727_0 3.8 MB r-mgcv-1.8_28 | r36h96ca727_0 2.6 MB r-munsell-0.5.0 | r36h6115d3f_0 254 KB r-nlme-3.1_139 | r36ha65eedd_0 2.2 MB r-pillar-1.3.1 | r36h6115d3f_0 180 KB r-pkgconfig-2.0.2 | r36h6115d3f_0 25 KB r-plyr-1.8.4 | r36h29659fb_0 815 KB r-r6-2.4.0 | r36h6115d3f_0 68 KB r-rcolorbrewer-1.1_2 | r36h6115d3f_0 62 KB r-rcpp-1.0.1 | r36h29659fb_0 3.3 MB r-reshape-0.8.8 | r36h6115d3f_0 174 KB r-reshape2-1.4.3 | r36h29659fb_0 129 KB r-rlang-0.3.4 | r36h96ca727_0 1.0 MB r-scales-1.0.0 | r36h29659fb_0 580 KB r-stringi-1.4.3 | r36h29659fb_0 773 KB r-stringr-1.4.0 | r36h6115d3f_0 221 KB r-tibble-2.1.1 | r36h96ca727_0 316 KB r-utf8-1.1.4 | r36h96ca727_0 159 KB r-viridislite-0.3.0 | r36h6115d3f_0 66 KB r-withr-2.1.2 | r36h6115d3f_0 181 KB setuptools-45.1.0 | py38_0 657 KB sqlite-3.30.1 | h7b6447c_0 1.9 MB wheel-0.34.1 | py38_0 49 KB ------------------------------------------------------------ Total: 92.5 MB The following NEW packages will be INSTALLED: certifi pkgs/main/linux-64::certifi-2019.11.28-py38_0 gatk bioconda/noarch::gatk-3.8-7 pip pkgs/main/linux-64::pip-20.0.2-py38_1 python pkgs/main/linux-64::python-3.8.1-h0371630_1 r-assertthat pkgs/r/noarch::r-assertthat-0.2.1-r36h6115d3f_0 r-bitops pkgs/r/linux-64::r-bitops-1.0_6-r36h96ca727_4 r-catools pkgs/r/linux-64::r-catools-1.17.1.2-r36h29659fb_0 r-cli pkgs/r/noarch::r-cli-1.1.0-r36h6115d3f_0 r-colorspace pkgs/r/linux-64::r-colorspace-1.4_1-r36h96ca727_0 r-crayon pkgs/r/noarch::r-crayon-1.3.4-r36h6115d3f_0 r-dichromat pkgs/r/noarch::r-dichromat-2.0_0-r36h6115d3f_4 r-digest pkgs/r/linux-64::r-digest-0.6.18-r36h96ca727_0 r-fansi pkgs/r/linux-64::r-fansi-0.4.0-r36h96ca727_0 r-gdata pkgs/r/noarch::r-gdata-2.18.0-r36h6115d3f_0 r-ggplot2 pkgs/r/noarch::r-ggplot2-3.1.1-r36h6115d3f_0 r-glue pkgs/r/linux-64::r-glue-1.3.1-r36h96ca727_0 r-gplots pkgs/r/noarch::r-gplots-3.0.1.1-r36h6115d3f_0 r-gsalib pkgs/r/noarch::r-gsalib-2.1-r36h6115d3f_0 r-gtable pkgs/r/noarch::r-gtable-0.3.0-r36h6115d3f_0 r-gtools pkgs/r/linux-64::r-gtools-3.8.1-r36h96ca727_0 r-kernsmooth pkgs/r/linux-64::r-kernsmooth-2.23_15-r36ha65eedd_4 r-labeling pkgs/r/noarch::r-labeling-0.3-r36h6115d3f_4 r-lattice pkgs/r/linux-64::r-lattice-0.20_38-r36h96ca727_0 r-lazyeval pkgs/r/linux-64::r-lazyeval-0.2.2-r36h96ca727_0 r-magrittr pkgs/r/noarch::r-magrittr-1.5-r36h6115d3f_4 r-mass pkgs/r/linux-64::r-mass-7.3_51.3-r36h96ca727_0 r-matrix pkgs/r/linux-64::r-matrix-1.2_17-r36h96ca727_0 r-mgcv pkgs/r/linux-64::r-mgcv-1.8_28-r36h96ca727_0 r-munsell pkgs/r/noarch::r-munsell-0.5.0-r36h6115d3f_0 r-nlme pkgs/r/linux-64::r-nlme-3.1_139-r36ha65eedd_0 r-pillar pkgs/r/noarch::r-pillar-1.3.1-r36h6115d3f_0 r-pkgconfig pkgs/r/noarch::r-pkgconfig-2.0.2-r36h6115d3f_0 r-plyr pkgs/r/linux-64::r-plyr-1.8.4-r36h29659fb_0 r-r6 pkgs/r/noarch::r-r6-2.4.0-r36h6115d3f_0 r-rcolorbrewer pkgs/r/noarch::r-rcolorbrewer-1.1_2-r36h6115d3f_0 r-rcpp pkgs/r/linux-64::r-rcpp-1.0.1-r36h29659fb_0 r-reshape pkgs/r/linux-64::r-reshape-0.8.8-r36h6115d3f_0 r-reshape2 pkgs/r/linux-64::r-reshape2-1.4.3-r36h29659fb_0 r-rlang pkgs/r/linux-64::r-rlang-0.3.4-r36h96ca727_0 r-scales pkgs/r/linux-64::r-scales-1.0.0-r36h29659fb_0 r-stringi pkgs/r/linux-64::r-stringi-1.4.3-r36h29659fb_0 r-stringr pkgs/r/noarch::r-stringr-1.4.0-r36h6115d3f_0 r-tibble pkgs/r/linux-64::r-tibble-2.1.1-r36h96ca727_0 r-utf8 pkgs/r/linux-64::r-utf8-1.1.4-r36h96ca727_0 r-viridislite pkgs/r/noarch::r-viridislite-0.3.0-r36h6115d3f_0 r-withr pkgs/r/noarch::r-withr-2.1.2-r36h6115d3f_0 setuptools pkgs/main/linux-64::setuptools-45.1.0-py38_0 sqlite pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0 wheel pkgs/main/linux-64::wheel-0.34.1-py38_0 Proceed ([y]/n)? y Downloading and Extracting Packages pip-20.0.2 | 1.9 MB | ############################################################ | 100% r-glue-1.3.1 | 165 KB | ############################################################ | 100% r-cli-1.1.0 | 189 KB | ############################################################ | 100% r-gsalib-2.1 | 31 KB | ############################################################ | 100% r-munsell-0.5.0 | 254 KB | ############################################################ | 100% r-bitops-1.0_6 | 34 KB | ############################################################ | 100% r-reshape2-1.4.3 | 129 KB | ############################################################ | 100% r-rcpp-1.0.1 | 3.3 MB | ############################################################ | 100% r-lattice-0.20_38 | 1.1 MB | ############################################################ | 100% r-colorspace-1.4_1 | 2.5 MB | ############################################################ | 100% r-gdata-2.18.0 | 1.1 MB | ############################################################ | 100% r-scales-1.0.0 | 580 KB | ############################################################ | 100% r-withr-2.1.2 | 181 KB | ############################################################ | 100% r-matrix-1.2_17 | 3.8 MB | ############################################################ | 100% r-mass-7.3_51.3 | 1.1 MB | ############################################################ | 100% r-mgcv-1.8_28 | 2.6 MB | ############################################################ | 100% setuptools-45.1.0 | 657 KB | ############################################################ | 100% r-labeling-0.3 | 71 KB | ############################################################ | 100% r-lazyeval-0.2.2 | 164 KB | ############################################################ | 100% gatk-3.8 | 8 KB | ############################################################ | 100% certifi-2019.11.28 | 156 KB | ############################################################ | 100% r-dichromat-2.0_0 | 163 KB | ############################################################ | 100% r-gtable-0.3.0 | 425 KB | ############################################################ | 100% r-r6-2.4.0 | 68 KB | ############################################################ | 100% r-tibble-2.1.1 | 316 KB | ############################################################ | 100% r-reshape-0.8.8 | 174 KB | ############################################################ | 100% r-kernsmooth-2.23_15 | 102 KB | ############################################################ | 100% r-plyr-1.8.4 | 815 KB | ############################################################ | 100% r-fansi-0.4.0 | 193 KB | ############################################################ | 100% r-rcolorbrewer-1.1_2 | 62 KB | ############################################################ | 100% r-viridislite-0.3.0 | 66 KB | ############################################################ | 100% r-magrittr-1.5 | 173 KB | ############################################################ | 100% wheel-0.34.1 | 49 KB | ############################################################ | 100% r-pkgconfig-2.0.2 | 25 KB | ############################################################ | 100% python-3.8.1 | 57.8 MB | ############################################################ | 100% sqlite-3.30.1 | 1.9 MB | ############################################################ | 100% r-rlang-0.3.4 | 1.0 MB | ############################################################ | 100% r-assertthat-0.2.1 | 74 KB | ############################################################ | 100% r-utf8-1.1.4 | 159 KB | ############################################################ | 100% r-stringr-1.4.0 | 221 KB | ############################################################ | 100% r-catools-1.17.1.2 | 223 KB | ############################################################ | 100% r-gplots-3.0.1.1 | 699 KB | ############################################################ | 100% r-ggplot2-3.1.1 | 3.6 MB | ############################################################ | 100% r-gtools-3.8.1 | 325 KB | ############################################################ | 100% r-pillar-1.3.1 | 180 KB | ############################################################ | 100% r-nlme-3.1_139 | 2.2 MB | ############################################################ | 100% r-digest-0.6.18 | 155 KB | ############################################################ | 100% r-stringi-1.4.3 | 773 KB | ############################################################ | 100% r-crayon-1.3.4 | 757 KB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install bedtools Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - bedtools The following packages will be downloaded: package | build ---------------------------|----------------- bedtools-2.29.2 | hc088bd4_0 13.8 MB bioconda ------------------------------------------------------------ Total: 13.8 MB The following NEW packages will be INSTALLED: bedtools bioconda/linux-64::bedtools-2.29.2-hc088bd4_0 Proceed ([y]/n)? y Downloading and Extracting Packages bedtools-2.29.2 | 13.8 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install SnpEff Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - snpeff The following packages will be downloaded: package | build ---------------------------|----------------- snpeff-4.3.1t | 3 19.7 MB bioconda ------------------------------------------------------------ Total: 19.7 MB The following NEW packages will be INSTALLED: snpeff bioconda/noarch::snpeff-4.3.1t-3 Proceed ([y]/n)? t Invalid choice: t Proceed ([y]/n)? y Downloading and Extracting Packages snpeff-4.3.1t | 19.7 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40804/bash-command-to-install-bwa-samtools-picard Sat, 01 Feb 2020 01:55:04 -0600 https://bioinformaticsonline.com/snippets/view/40804/bash-command-to-install-bwa-samtools-picard (base) [wsu29@bladeamd-2 tmp]$ conda install bwa Collecting package metadata (repodata.json): done Solving environment: - The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: - defaults/linux-64::numba==0.43.1=py37h962f231_0 - defaults/linux-64::anaconda==2019.03=py37_0 done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3 added / updated specs: - bwa The following packages will be downloaded: package | build ---------------------------|----------------- _anaconda_depends-2019.03 | py37_0 5 KB anaconda-custom | py37_1 3 KB bwa-0.7.17 | hed695b0_7 523 KB bioconda ca-certificates-2020.1.1 | 0 132 KB certifi-2019.11.28 | py37_0 156 KB openssl-1.1.1d | h7b6447c_3 3.7 MB perl-5.26.2 | h14c3975_0 15.9 MB tbb-2019.8 | hfd86e86_0 1.4 MB ------------------------------------------------------------ Total: 21.8 MB The following NEW packages will be INSTALLED: _anaconda_depends pkgs/main/linux-64::_anaconda_depends-2019.03-py37_0 bwa bioconda/linux-64::bwa-0.7.17-hed695b0_7 perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0 tbb pkgs/main/linux-64::tbb-2019.8-hfd86e86_0 The following packages will be UPDATED: ca-certificates 2019.1.23-0 --> 2020.1.1-0 certifi 2019.3.9-py37_0 --> 2019.11.28-py37_0 openssl 1.1.1b-h7b6447c_1 --> 1.1.1d-h7b6447c_3 The following packages will be DOWNGRADED: anaconda 2019.03-py37_0 --> custom-py37_1 Proceed ([y]/n)? y Downloading and Extracting Packages certifi-2019.11.28 | 156 KB | ############################################################ | 100% ca-certificates-2020 | 132 KB | ############################################################ | 100% perl-5.26.2 | 15.9 MB | ############################################################ | 100% bwa-0.7.17 | 523 KB | ############################################################ | 100% anaconda-custom | 3 KB | ############################################################ | 100% openssl-1.1.1d | 3.7 MB | ############################################################ | 100% _anaconda_depends-20 | 5 KB | ############################################################ | 100% tbb-2019.8 | 1.4 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install samtools Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - samtools The following packages will be downloaded: package | build ---------------------------|----------------- bzip2-1.0.8 | h7b6447c_0 105 KB curl-7.67.0 | hbc83047_0 145 KB htslib-1.9 | h4da6232_3 1.2 MB bioconda krb5-1.16.4 | h173b8e3_0 1.4 MB libcurl-7.67.0 | h20c2e04_0 576 KB libdeflate-1.2 | h516909a_1 63 KB bioconda libssh2-1.8.2 | h1ba5d50_0 250 KB libstdcxx-ng-9.1.0 | hdf63c60_0 4.0 MB samtools-1.9 | h10a08f8_12 299 KB bioconda ------------------------------------------------------------ Total: 8.0 MB The following NEW packages will be INSTALLED: bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0 curl pkgs/main/linux-64::curl-7.67.0-hbc83047_0 htslib bioconda/linux-64::htslib-1.9-h4da6232_3 krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0 libcurl pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libdeflate bioconda/linux-64::libdeflate-1.2-h516909a_1 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libssh2 pkgs/main/linux-64::libssh2-1.8.2-h1ba5d50_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3 samtools bioconda/linux-64::samtools-1.9-h10a08f8_12 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4 Proceed ([y]/n)? y Downloading and Extracting Packages libstdcxx-ng-9.1.0 | 4.0 MB | ############################################################ | 100% libdeflate-1.2 | 63 KB | ############################################################ | 100% bzip2-1.0.8 | 105 KB | ############################################################ | 100% libssh2-1.8.2 | 250 KB | ############################################################ | 100% samtools-1.9 | 299 KB | ############################################################ | 100% krb5-1.16.4 | 1.4 MB | ############################################################ | 100% libcurl-7.67.0 | 576 KB | ############################################################ | 100% curl-7.67.0 | 145 KB | ############################################################ | 100% htslib-1.9 | 1.2 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install picard Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - picard The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.0 | anacondar_1 2 KB binutils_impl_linux-64-2.33.1| he6710b0_7 8.6 MB binutils_linux-64-2.33.1 | h9595d00_15 24 KB bwidget-1.9.11 | 1 113 KB gcc_impl_linux-64-7.3.0 | habb00fd_1 73.2 MB gcc_linux-64-7.3.0 | h553295d_15 25 KB gfortran_impl_linux-64-7.3.0| hdf63c60_1 9.0 MB gfortran_linux-64-7.3.0 | h553295d_15 25 KB glib-2.63.1 | h5a9c865_0 3.4 MB gsl-2.4 | h14c3975_4 2.6 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 18.7 MB gxx_linux-64-7.3.0 | h553295d_15 25 KB ld_impl_linux-64-2.33.1 | h53a641e_7 645 KB libpng-1.6.37 | hbc83047_0 364 KB libtiff-4.1.0 | h2733197_0 589 KB libxml2-2.9.9 | hea5a465_1 2.0 MB make-4.2.1 | h1bed415_1 429 KB openjdk-8.0.152 | h46b5887_1 128.6 MB picard-2.21.7 | 0 14.7 MB bioconda r-base-3.6.1 | h9bb98a2_1 39.7 MB tktable-2.10 | h14c3975_0 88 KB ------------------------------------------------------------ Total: 302.7 MB The following NEW packages will be INSTALLED: _r-mutex pkgs/r/linux-64::_r-mutex-1.0.0-anacondar_1 binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.33.1-he6710b0_7 binutils_linux-64 pkgs/main/linux-64::binutils_linux-64-2.33.1-h9595d00_15 bwidget pkgs/main/linux-64::bwidget-1.9.11-1 cairo pkgs/main/linux-64::cairo-1.14.12-h8948797_3 fontconfig pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0 freetype pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1 fribidi pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 pkgs/main/linux-64::gcc_linux-64-7.3.0-h553295d_15 gfortran_impl_lin~ pkgs/main/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_1 gfortran_linux-64 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl pkgs/main/linux-64::gsl-2.4-h14c3975_4 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 pkgs/main/linux-64::gxx_linux-64-7.3.0-h553295d_15 harfbuzz pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0 icu pkgs/main/linux-64::icu-58.2-h9c2bf20_1 jpeg pkgs/main/linux-64::jpeg-9b-h024ee3a_2 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0 libuuid pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2 libxcb pkgs/main/linux-64::libxcb-1.13-h1bed415_1 libxml2 pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1 make pkgs/main/linux-64::make-4.2.1-h1bed415_1 openjdk pkgs/main/linux-64::openjdk-8.0.152-h46b5887_1 pango pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 picard bioconda/noarch::picard-2.21.7-0 pixman pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0 r-base pkgs/r/linux-64::r-base-3.6.1-h9bb98a2_1 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0 Proceed ([y]/n)? y Downloading and Extracting Packages tktable-2.10 | 88 KB | ############################################################ | 100% gcc_linux-64-7.3.0 | 25 KB | ############################################################ | 100% openjdk-8.0.152 | 128.6 MB | ############################################################ | 100% gfortran_impl_linux- | 9.0 MB | ############################################################ | 100% libpng-1.6.37 | 364 KB | ############################################################ | 100% libxml2-2.9.9 | 2.0 MB | ############################################################ | 100% gcc_impl_linux-64-7. | 73.2 MB | ############################################################ | 100% picard-2.21.7 | 14.7 MB | ############################################################ | 100% gsl-2.4 | 2.6 MB | ############################################################ | 100% r-base-3.6.1 | 39.7 MB | ############################################################ | 100% ld_impl_linux-64-2.3 | 645 KB | ############################################################ | 100% _r-mutex-1.0.0 | 2 KB | ############################################################ | 100% bwidget-1.9.11 | 113 KB | ############################################################ | 100% make-4.2.1 | 429 KB | ############################################################ | 100% glib-2.63.1 | 3.4 MB | ############################################################ | 100% gxx_linux-64-7.3.0 | 25 KB | ############################################################ | 100% binutils_linux-64-2. | 24 KB | ############################################################ | 100% gxx_impl_linux-64-7. | 18.7 MB | ############################################################ | 100% gfortran_linux-64-7. | 25 KB | ############################################################ | 100% libtiff-4.1.0 | 589 KB | ############################################################ | 100% binutils_impl_linux- | 8.6 MB | ############################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40803/bash-command-to-install-miniconda Sat, 01 Feb 2020 01:46:31 -0600 https://bioinformaticsonline.com/snippets/view/40803/bash-command-to-install-miniconda (base) [wsu29@bladeamd-2 tmp]$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh --2020-02-01 13:25:25-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Resolving repo.anaconda.com... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8303, ... Connecting to repo.anaconda.com|104.16.130.3|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 71785000 (68M) [application/x-sh] Saving to: `Miniconda3-latest-Linux-x86_64.sh' 100%[=============================================================>] 7,17,85,000 2.07M/s in 33s 2020-02-01 13:25:59 (2.06 MB/s) - `Miniconda3-latest-Linux-x86_64.sh' saved [71785000/71785000] (base) [wsu29@bladeamd-2 tmp]$ sh Miniconda3-latest-Linux-x86_64.sh Welcome to Miniconda3 4.7.12 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> ... ... ... Please answer 'yes' or 'no':' >>> yes Miniconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/miniconda3] >>> Miniconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/miniconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/miniconda3] >>> PREFIX=/data/sata_data/workshop/wsu29/miniconda3 Unpacking payload ... Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /data/sata_data/workshop/wsu29/miniconda3 added / updated specs: - _libgcc_mutex==0.1=main - asn1crypto==1.2.0=py37_0 - ca-certificates==2019.10.16=0 - certifi==2019.9.11=py37_0 - cffi==1.13.0=py37h2e261b9_0 - chardet==3.0.4=py37_1003 - conda-package-handling==1.6.0=py37h7b6447c_0 - conda==4.7.12=py37_0 - cryptography==2.8=py37h1ba5d50_0 - idna==2.8=py37_0 - libedit==3.1.20181209=hc058e9b_0 - libffi==3.2.1=hd88cf55_4 - libgcc-ng==9.1.0=hdf63c60_0 - libstdcxx-ng==9.1.0=hdf63c60_0 - ncurses==6.1=he6710b0_1 - openssl==1.1.1d=h7b6447c_3 - pip==19.3.1=py37_0 - pycosat==0.6.3=py37h14c3975_0 - pycparser==2.19=py37_0 - pyopenssl==19.0.0=py37_0 - pysocks==1.7.1=py37_0 - python==3.7.4=h265db76_1 - readline==7.0=h7b6447c_5 - requests==2.22.0=py37_0 - ruamel_yaml==0.15.46=py37h14c3975_0 - setuptools==41.4.0=py37_0 - six==1.12.0=py37_0 - sqlite==3.30.0=h7b6447c_0 - tk==8.6.8=hbc83047_0 - tqdm==4.36.1=py_0 - urllib3==1.24.2=py37_0 - wheel==0.33.6=py37_0 - xz==5.2.4=h14c3975_4 - yaml==0.1.7=had09818_2 - zlib==1.2.11=h7b6447c_3 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main asn1crypto pkgs/main/linux-64::asn1crypto-1.2.0-py37_0 ca-certificates pkgs/main/linux-64::ca-certificates-2019.10.16-0 certifi pkgs/main/linux-64::certifi-2019.9.11-py37_0 cffi pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0 chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003 conda pkgs/main/linux-64::conda-4.7.12-py37_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0 cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0 idna pkgs/main/linux-64::idna-2.8-py37_0 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3 pip pkgs/main/linux-64::pip-19.3.1-py37_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0 pycparser pkgs/main/linux-64::pycparser-2.19-py37_0 pyopenssl pkgs/main/linux-64::pyopenssl-19.0.0-py37_0 pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0 python pkgs/main/linux-64::python-3.7.4-h265db76_1 readline pkgs/main/linux-64::readline-7.0-h7b6447c_5 requests pkgs/main/linux-64::requests-2.22.0-py37_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0 setuptools pkgs/main/linux-64::setuptools-41.4.0-py37_0 six pkgs/main/linux-64::six-1.12.0-py37_0 sqlite pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0 tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.36.1-py_0 urllib3 pkgs/main/linux-64::urllib3-1.24.2-py37_0 wheel pkgs/main/linux-64::wheel-0.33.6-py37_0 xz pkgs/main/linux-64::xz-5.2.4-h14c3975_4 yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Preparing transaction: done Executing transaction: done installation finished. Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no] [no] >>> yes no change /data/sata_data/workshop/wsu29/miniconda3/condabin/conda no change /data/sata_data/workshop/wsu29/miniconda3/bin/conda no change /data/sata_data/workshop/wsu29/miniconda3/bin/conda-env no change /data/sata_data/workshop/wsu29/miniconda3/bin/activate no change /data/sata_data/workshop/wsu29/miniconda3/bin/deactivate no change /data/sata_data/workshop/wsu29/miniconda3/etc/profile.d/conda.sh no change /data/sata_data/workshop/wsu29/miniconda3/etc/fish/conf.d/conda.fish no change /data/sata_data/workshop/wsu29/miniconda3/shell/condabin/Conda.psm1 no change /data/sata_data/workshop/wsu29/miniconda3/shell/condabin/conda-hook.ps1 no change /data/sata_data/workshop/wsu29/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh no change /data/sata_data/workshop/wsu29/miniconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing Miniconda3!]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40802/bash-commandline-to-install-anaconda Sat, 01 Feb 2020 01:36:00 -0600 https://bioinformaticsonline.com/snippets/view/40802/bash-commandline-to-install-anaconda #The line begins with $ are the commands $ mkdir tmp $ cd tmp/ $ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 654M 100 654M 0 0 940k 0 0:11:52 0:11:52 --:--:-- 2059k $ sha256sum Anaconda3-2019.03-Linux-x86_64.sh 45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a Anaconda3-2019.03-Linux-x86_64.sh $ bash Anaconda3-2019.03-Linux-x86_64.sh In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> =================================== Anaconda End User License Agreement =================================== ...... ...... ...... Do you accept the license terms? [yes|no] Please answer 'yes' or 'no':' >>> yes Anaconda3 will now be installed into this location: /data/sata_data/workshop/wsu29/anaconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/data/sata_data/workshop/wsu29/anaconda3] >>> PREFIX=/data/sata_data/workshop/wsu29/anaconda3 installing: python-3.7.3-h0371630_0 ... Python 3.7.3 installing: conda-env-2.6.0-1 ... installing: blas-1.0-mkl ... installing: ca-certificates-2019.1.23-0 ... installing: intel-openmp-2019.3-199 ... installing: libgcc-ng-8.2.0-hdf63c60_1 ... installing: libgfortran-ng-7.3.0-hdf63c60_0 ... installing: libstdcxx-ng-8.2.0-hdf63c60_1 ... installing: bzip2-1.0.6-h14c3975_5 ... installing: expat-2.2.6-he6710b0_0 ... installing: fribidi-1.0.5-h7b6447c_0 ... installing: gmp-6.1.2-h6c8ec71_1 ... installing: graphite2-1.3.13-h23475e2_0 ... installing: icu-58.2-h9c2bf20_1 ... installing: jbig-2.1-hdba287a_0 ... installing: jpeg-9b-h024ee3a_2 ... installing: libffi-3.2.1-hd88cf55_4 ... installing: liblief-0.9.0-h7725739_2 ... installing: libsodium-1.0.16-h1bed415_0 ... installing: libtool-2.4.6-h7b6447c_5 ... installing: libuuid-1.0.3-h1bed415_2 ... installing: libxcb-1.13-h1bed415_1 ... installing: lz4-c-1.8.1.2-h14c3975_0 ... installing: lzo-2.10-h49e0be7_2 ... installing: mkl-2019.3-199 ... installing: ncurses-6.1-he6710b0_1 ... installing: openssl-1.1.1b-h7b6447c_1 ... installing: patchelf-0.9-he6710b0_3 ... installing: pcre-8.43-he6710b0_0 ... installing: pixman-0.38.0-h7b6447c_0 ... installing: snappy-1.1.7-hbae5bb6_3 ... installing: xz-5.2.4-h14c3975_4 ... installing: yaml-0.1.7-had09818_2 ... installing: zlib-1.2.11-h7b6447c_3 ... installing: blosc-1.15.0-hd408876_0 ... installing: glib-2.56.2-hd408876_0 ... installing: hdf5-1.10.4-hb1b8bf9_0 ... installing: libedit-3.1.20181209-hc058e9b_0 ... installing: libpng-1.6.36-hbc83047_0 ... installing: libssh2-1.8.0-h1ba5d50_4 ... installing: libxml2-2.9.9-he19cac6_0 ... installing: mpfr-4.0.1-hdf1c602_3 ... installing: pandoc-2.2.3.2-0 ... installing: readline-7.0-h7b6447c_5 ... installing: tk-8.6.8-hbc83047_0 ... installing: zeromq-4.3.1-he6710b0_3 ... installing: zstd-1.3.7-h0b5b093_0 ... installing: dbus-1.13.6-h746ee38_0 ... installing: freetype-2.9.1-h8a8886c_1 ... installing: gstreamer-1.14.0-hb453b48_1 ... installing: krb5-1.16.1-h173b8e3_7 ... installing: libarchive-3.3.3-h5d8350f_5 ... installing: libtiff-4.0.10-h2733197_2 ... installing: libxslt-1.1.33-h7d1a2b0_0 ... installing: mpc-1.1.0-h10f8cd9_1 ... installing: sqlite-3.27.2-h7b6447c_0 ... installing: unixodbc-2.3.7-h14c3975_0 ... installing: fontconfig-2.13.0-h9420a91_0 ... installing: gst-plugins-base-1.14.0-hbbd80ab_1 ... installing: libcurl-7.64.0-h20c2e04_2 ... installing: alabaster-0.7.12-py37_0 ... installing: asn1crypto-0.24.0-py37_0 ... installing: atomicwrites-1.3.0-py37_1 ... installing: attrs-19.1.0-py37_1 ... installing: backcall-0.1.0-py37_0 ... installing: backports-1.0-py37_1 ... installing: bitarray-0.8.3-py37h14c3975_0 ... installing: boto-2.49.0-py37_0 ... installing: cairo-1.14.12-h8948797_3 ... installing: certifi-2019.3.9-py37_0 ... installing: chardet-3.0.4-py37_1 ... installing: click-7.0-py37_0 ... installing: cloudpickle-0.8.0-py37_0 ... installing: colorama-0.4.1-py37_0 ... installing: contextlib2-0.5.5-py37_0 ... installing: curl-7.64.0-hbc83047_2 ... installing: dask-core-1.1.4-py37_1 ... installing: decorator-4.4.0-py37_1 ... installing: defusedxml-0.5.0-py37_1 ... installing: docutils-0.14-py37_0 ... installing: entrypoints-0.3-py37_0 ... installing: et_xmlfile-1.0.1-py37_0 ... installing: fastcache-1.0.2-py37h14c3975_2 ... installing: filelock-3.0.10-py37_0 ... installing: future-0.17.1-py37_0 ... installing: glob2-0.6-py37_1 ... installing: gmpy2-2.0.8-py37h10f8cd9_2 ... installing: greenlet-0.4.15-py37h7b6447c_0 ... installing: heapdict-1.0.0-py37_2 ... installing: idna-2.8-py37_0 ... installing: imagesize-1.1.0-py37_0 ... installing: ipython_genutils-0.2.0-py37_0 ... installing: itsdangerous-1.1.0-py37_0 ... installing: jdcal-1.4-py37_0 ... installing: jeepney-0.4-py37_0 ... installing: kiwisolver-1.0.1-py37hf484d3e_0 ... installing: lazy-object-proxy-1.3.1-py37h14c3975_2 ... installing: llvmlite-0.28.0-py37hd408876_0 ... installing: locket-0.2.0-py37_1 ... installing: lxml-4.3.2-py37hefd8a0e_0 ... installing: markupsafe-1.1.1-py37h7b6447c_0 ... installing: mccabe-0.6.1-py37_1 ... installing: mistune-0.8.4-py37h7b6447c_0 ... installing: mkl-service-1.1.2-py37he904b0f_5 ... installing: more-itertools-6.0.0-py37_0 ... installing: mpmath-1.1.0-py37_0 ... installing: msgpack-python-0.6.1-py37hfd86e86_1 ... installing: numpy-base-1.16.2-py37hde5b4d6_0 ... installing: olefile-0.46-py37_0 ... installing: pandocfilters-1.4.2-py37_1 ... installing: parso-0.3.4-py37_0 ... installing: pep8-1.7.1-py37_0 ... installing: pickleshare-0.7.5-py37_0 ... installing: pkginfo-1.5.0.1-py37_0 ... installing: pluggy-0.9.0-py37_0 ... installing: ply-3.11-py37_0 ... installing: prometheus_client-0.6.0-py37_0 ... installing: psutil-5.6.1-py37h7b6447c_0 ... installing: ptyprocess-0.6.0-py37_0 ... installing: py-1.8.0-py37_0 ... installing: py-lief-0.9.0-py37h7725739_2 ... installing: pycodestyle-2.5.0-py37_0 ... installing: pycosat-0.6.3-py37h14c3975_0 ... installing: pycparser-2.19-py37_0 ... installing: pycrypto-2.6.1-py37h14c3975_9 ... installing: pycurl-7.43.0.2-py37h1ba5d50_0 ... installing: pyflakes-2.1.1-py37_0 ... installing: pyodbc-4.0.26-py37he6710b0_0 ... installing: pyparsing-2.3.1-py37_0 ... installing: pysocks-1.6.8-py37_0 ... installing: python-libarchive-c-2.8-py37_6 ... installing: pytz-2018.9-py37_0 ... installing: pyyaml-5.1-py37h7b6447c_0 ... installing: pyzmq-18.0.0-py37he6710b0_0 ... installing: qt-5.9.7-h5867ecd_1 ... installing: qtpy-1.7.0-py37_1 ... installing: rope-0.12.0-py37_0 ... installing: ruamel_yaml-0.15.46-py37h14c3975_0 ... installing: send2trash-1.5.0-py37_0 ... installing: simplegeneric-0.8.1-py37_2 ... installing: sip-4.19.8-py37hf484d3e_0 ... installing: six-1.12.0-py37_0 ... installing: snowballstemmer-1.2.1-py37_0 ... installing: sortedcontainers-2.1.0-py37_0 ... installing: soupsieve-1.8-py37_0 ... installing: sphinxcontrib-1.0-py37_1 ... installing: sqlalchemy-1.3.1-py37h7b6447c_0 ... installing: tblib-1.3.2-py37_0 ... installing: testpath-0.4.2-py37_0 ... installing: toolz-0.9.0-py37_0 ... installing: tornado-6.0.2-py37h7b6447c_0 ... installing: tqdm-4.31.1-py37_1 ... installing: unicodecsv-0.14.1-py37_0 ... installing: wcwidth-0.1.7-py37_0 ... installing: webencodings-0.5.1-py37_1 ... installing: werkzeug-0.14.1-py37_0 ... installing: wrapt-1.11.1-py37h7b6447c_0 ... installing: wurlitzer-1.0.2-py37_0 ... installing: xlrd-1.2.0-py37_0 ... installing: xlsxwriter-1.1.5-py37_0 ... installing: xlwt-1.3.0-py37_0 ... installing: zipp-0.3.3-py37_1 ... installing: babel-2.6.0-py37_0 ... installing: backports.os-0.1.1-py37_0 ... installing: backports.shutil_get_terminal_size-1.0.0-py37_2 ... installing: beautifulsoup4-4.7.1-py37_1 ... installing: cffi-1.12.2-py37h2e261b9_1 ... installing: cycler-0.10.0-py37_0 ... installing: cytoolz-0.9.0.1-py37h14c3975_1 ... installing: harfbuzz-1.8.8-hffaf4a1_0 ... installing: html5lib-1.0.1-py37_0 ... installing: importlib_metadata-0.8-py37_0 ... installing: jedi-0.13.3-py37_0 ... 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Do you wish the installer to initialize Anaconda3 by running conda init? [yes|no] [no] >>> yes WARNING: The conda.compat module is deprecated and will be removed in a future release. no change /data/sata_data/workshop/wsu29/anaconda3/condabin/conda no change /data/sata_data/workshop/wsu29/anaconda3/bin/conda no change /data/sata_data/workshop/wsu29/anaconda3/bin/conda-env no change /data/sata_data/workshop/wsu29/anaconda3/bin/activate no change /data/sata_data/workshop/wsu29/anaconda3/bin/deactivate no change /data/sata_data/workshop/wsu29/anaconda3/etc/profile.d/conda.sh no change /data/sata_data/workshop/wsu29/anaconda3/etc/fish/conf.d/conda.fish no change /data/sata_data/workshop/wsu29/anaconda3/shell/condabin/Conda.psm1 no change /data/sata_data/workshop/wsu29/anaconda3/shell/condabin/conda-hook.ps1 no change /data/sata_data/workshop/wsu29/anaconda3/lib/python3.7/site-packages/xonsh/conda.xsh no change /data/sata_data/workshop/wsu29/anaconda3/etc/profile.d/conda.csh modified /data/sata_data/workshop/wsu29/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing Anaconda3! =========================================================================== Anaconda and JetBrains are working together to bring you Anaconda-powered environments tightly integrated in the PyCharm IDE. PyCharm for Anaconda is available at: https://www.anaconda.com/pycharm #Ativate now $ source ~/.bashrc #Check/Test $ conda list # Python 3 environment named my_env can be created with the following command: $ conda create --name my_env python=3 #Activate env $ conda activate my_env #To update conda $ conda update -n base -c defaults conda]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40623/perl-script-to-remove-duplicated-lines Mon, 27 Jan 2020 04:48:56 -0600 https://bioinformaticsonline.com/snippets/view/40623/perl-script-to-remove-duplicated-lines #!/usr/bin/perl use strict; use warnings; { $_ = <DATA>; my $next_line; while( $next_line = <DATA> ) { #print "current line: $_ -- next line: $next_line$/"; print $_ if $_ ne $next_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ apple apple plum vinegar apple banana banana banana apple]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/40571/perl-subroutine-to-creating-kmer Mon, 20 Jan 2020 04:32:32 -0600 https://bioinformaticsonline.com/snippets/view/40571/perl-subroutine-to-creating-kmer sub k_mers { my ($sequence, $k) = @_; my $len = length($sequence); my @result = (); for (my $i = 0; $i <= $len-$k; $i++) { push(@result, substr($sequence, $i, $k)); } return @result; }]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping Sun, 28 Apr 2019 12:37:57 -0500 https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/37682/perl-script-to-break-the-contigs-by-n Tue, 11 Sep 2018 15:31:55 -0500 https://bioinformaticsonline.com/snippets/view/37682/perl-script-to-break-the-contigs-by-n #!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "<$ARGV[0]", -format => 'fasta' ); my $minNlen = 5; my $out=Bio::SeqIO->new(-file=>">$ARGV[0].parts.fasta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff"); while ( my $seqobj = $fasta->next_seq() ) { #gets contig id my $contig = $seqobj->display_id(); #gets contig sequence my $seq = $seqobj->seq; my $lenseq=length $seq; $seq = uc $seq; #now all bases are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stores a hash from the contig id to the NNNNN regions found. #Each region is represented as a pair "$ini $end" indicating that start and #the end of the NNNNN region in the contig my @regions=(); my @bases=split //,$seq; push(@bases,"E"); #This extra position marks the end of the contig my $n=0; #Sorry for this loop, but its less memory expensive than regular expressions for (my $i=0;$i<=$#bases;$i++) { if ($bases[$i] eq 'N') { $n++; } else { if ($n>=$minNlen) { my $end=$i; my $ini=$end-$n+1; push(@regions,"$ini $end"); } $n=0; } } #Now, all regions without Ns are in @regions my $cont=1; my $laststart=1; if ($#regions>=0) { for (my $i=0;$i<=$#regions;$i++) { my ($ini,$end)=split /\s+/,$regions[$i]; my $cini=$laststart; my $cend=$ini-1; my $pseqobj=$seqobj->trunc($cini,$cend); my $new_id=$contig . "_p$cont"; $cont++; $pseqobj->display_id("$new_id"); $out->write_seq($pseqobj); print SCAFF "$new_id $cini $cend\n"; my $linksize=$end-$ini+1; print SCAFF "LINK $ini $end $linksize\n"; $laststart=$end+1; } my $lastregion=$regions[$#regions]; # print "$lastregion $#regions\n"; die; my ($ini,$end)= split /\s+/,$lastregion; if (($end+1)<$lenseq) { my $cini=$end+1; my $cend=$lenseq; my $pseqobj=$seqobj->trunc($end+1,$lenseq); my $new_id=$contig . "_p$cont"; $pseqobj->display_id("$new_id"); $out->write_seq($pseqobj); print SCAFF "$new_id $cini $cend\n"; } } else { $seqobj->display_id("$contig.1.1"); $out->write_seq($seqobj); print SCAFF "$contig.1.1 1 $lenseq\n"; } } close(SCAFF);]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/37489/perl-script-to-find-palindromic-pattern Mon, 06 Aug 2018 09:28:25 -0500 https://bioinformaticsonline.com/snippets/view/37489/perl-script-to-find-palindromic-pattern #!/usr/bin/perl use strict; use warnings; use strict; my %invert; @invert{ qw[ A C G T ] } = qw[ T G C A ]; my $in = do{ local $/; <DATA> }; chomp $in; print $in; for my $p1 ( 1 .. length( $in ) -2 ) { next unless substr( $in, $p1, 1 ) eq $invert{ substr $in, $p1+1, 1 }; my $pals = 0; for my $p2 ( 1 .. $p1 -1 ) { last unless substr( $in, $p1-$p2, 1 ) eq $invert{ substr $in, $p1+$p2+1, 1 }; ++$pals; } if( $pals ) { my $val=substr( $in, $p1-$pals, ($pals+1)*2 ); my $st=$p1-$pals; my $sLen=($pals+1)*2; my $ed=($st+$sLen)-1; print "$st\t$ed\t$sLen\t$val\n"; printf "%s%s at %d\n", ' 'x($p1-$pals), substr( $in, $p1-$pals, ($pals+1)*2 ), $p1-$pals; } } __DATA__ AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG]]> Rahul Nayak https://bioinformaticsonline.com/snippets/view/37227/perl-subroutine-to-read-genomereads-fasta-file Tue, 03 Jul 2018 04:56:15 -0500 https://bioinformaticsonline.com/snippets/view/37227/perl-subroutine-to-read-genomereads-fasta-file sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(<IN>){ chomp; if($_ =~ /^>/){ if(defined $id && defined $seq){ $map{$id} = $seq; $seq=""; } ($id) = split(' ',$_); $id=~s/>//; } else { $seq=$seq.$_; } } $map{$id} = $seq; close(IN); return \%map; }]]> Rahul Nayak