https://bioinformaticsonline.com/snippets/owner/lege?offset=40 https://bioinformaticsonline.com/snippets/view/43076/install-ragout-using-conda Wed, 16 Jun 2021 02:26:30 -0500 https://bioinformaticsonline.com/snippets/view/43076/install-ragout-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda ragout Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - ragout The following packages will be downloaded: package | build ---------------------------|----------------- decorator-4.3.0 | py37_0 16 KB networkx-2.2 | py37_1 1.6 MB ragout-2.3 | py37h22450f8_3 2.7 MB bioconda sibelia-3.0.7 | he1b5a44_2 24.8 MB bioconda ------------------------------------------------------------ Total: 29.2 MB The following NEW packages will be INSTALLED: decorator pkgs/main/linux-64::decorator-4.3.0-py37_0 networkx pkgs/main/linux-64::networkx-2.2-py37_1 ragout bioconda/linux-64::ragout-2.3-py37h22450f8_3 sibelia bioconda/linux-64::sibelia-3.0.7-he1b5a44_2 Proceed ([y]/n)? y Downloading and Extracting Packages networkx-2.2 | 1.6 MB | ################################################################################################################################################################## | 100% decorator-4.3.0 | 16 KB | ################################################################################################################################################################## | 100% sibelia-3.0.7 | 24.8 MB | ################################################################################################################################################################## | 100% ragout-2.3 | 2.7 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43075/install-assembly-stat-using-conda Wed, 16 Jun 2021 02:24:39 -0500 https://bioinformaticsonline.com/snippets/view/43075/install-assembly-stat-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda assembly-stats Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - assembly-stats The following packages will be downloaded: package | build ---------------------------|----------------- assembly-stats-1.0.1 | h7d875b9_4 29 KB bioconda ------------------------------------------------------------ Total: 29 KB The following NEW packages will be INSTALLED: assembly-stats bioconda/linux-64::assembly-stats-1.0.1-h7d875b9_4 Proceed ([y]/n)? y Downloading and Extracting Packages assembly-stats-1.0.1 | 29 KB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43074/install-gap2seq-using-conda Wed, 16 Jun 2021 02:22:24 -0500 https://bioinformaticsonline.com/snippets/view/43074/install-gap2seq-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 gap2seq Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - gap2seq The following packages will be downloaded: package | build ---------------------------|----------------- gap2seq-2.0 | boost1.61_1 4.6 MB bioconda/label/cf201901 ------------------------------------------------------------ Total: 4.6 MB The following NEW packages will be INSTALLED: libgcc pkgs/main/linux-64::libgcc-7.2.0-h69d50b8_2 The following packages will be SUPERSEDED by a higher-priority channel: gap2seq bioconda::gap2seq-3.1-py37h621e40c_0 --> bioconda/label/cf201901::gap2seq-2.0-boost1.61_1 Proceed ([y]/n)? y Downloading and Extracting Packages gap2seq-2.0 | 4.6 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43073/install-seqtk-using-conda Wed, 16 Jun 2021 02:19:55 -0500 https://bioinformaticsonline.com/snippets/view/43073/install-seqtk-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 seqtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - seqtk The following packages will be downloaded: package | build ---------------------------|----------------- seqtk-1.3 | ha92aebf_0 80 KB bioconda/label/cf201901 ------------------------------------------------------------ Total: 80 KB The following NEW packages will be INSTALLED: seqtk bioconda/label/cf201901/linux-64::seqtk-1.3-ha92aebf_0 Proceed ([y]/n)? y Downloading and Extracting Packages seqtk-1.3 | 80 KB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43072/install-minimap2-using-conda Wed, 16 Jun 2021 02:17:16 -0500 https://bioinformaticsonline.com/snippets/view/43072/install-minimap2-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda minimap2 Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - minimap2 The following packages will be downloaded: package | build ---------------------------|----------------- k8-0.2.5 | h9a82719_1 1.7 MB bioconda minimap2-2.20 | h5bf99c6_0 477 KB bioconda ------------------------------------------------------------ Total: 2.1 MB The following NEW packages will be INSTALLED: k8 bioconda/linux-64::k8-0.2.5-h9a82719_1 minimap2 bioconda/linux-64::minimap2-2.20-h5bf99c6_0 Proceed ([y]/n)? y Downloading and Extracting Packages k8-0.2.5 | 1.7 MB | ################################################################################################################################################################## | 100% minimap2-2.20 | 477 KB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43071/install-seqkit-using-conda Wed, 16 Jun 2021 02:15:47 -0500 https://bioinformaticsonline.com/snippets/view/43071/install-seqkit-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda seqkit Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - seqkit The following packages will be downloaded: package | build ---------------------------|----------------- seqkit-0.16.1 | h9ee0642_0 6.1 MB bioconda ------------------------------------------------------------ Total: 6.1 MB The following NEW packages will be INSTALLED: seqkit bioconda/linux-64::seqkit-0.16.1-h9ee0642_0 Proceed ([y]/n)? y Downloading and Extracting Packages seqkit-0.16.1 | 6.1 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43070/install-cvstk-using-codna Wed, 16 Jun 2021 02:11:23 -0500 https://bioinformaticsonline.com/snippets/view/43070/install-cvstk-using-codna vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda csvtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - csvtk The following packages will be downloaded: package | build ---------------------------|----------------- csvtk-0.23.0 | h9ee0642_0 7.2 MB bioconda ------------------------------------------------------------ Total: 7.2 MB The following NEW packages will be INSTALLED: csvtk bioconda/linux-64::csvtk-0.23.0-h9ee0642_0 Proceed ([y]/n)? y Downloading and Extracting Packages csvtk-0.23.0 | 7.2 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43069/install-shasta-using-conda Wed, 16 Jun 2021 02:09:25 -0500 https://bioinformaticsonline.com/snippets/view/43069/install-shasta-using-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda shasta Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - shasta The following packages will be downloaded: package | build ---------------------------|----------------- shasta-0.6.0 | hc9558a2_0 2.9 MB bioconda ------------------------------------------------------------ Total: 2.9 MB The following NEW packages will be INSTALLED: libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 shasta bioconda/linux-64::shasta-0.6.0-hc9558a2_0 Proceed ([y]/n)? y Downloading and Extracting Packages shasta-0.6.0 | 2.9 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/43068/install-canu-with-conda Wed, 16 Jun 2021 02:07:15 -0500 https://bioinformaticsonline.com/snippets/view/43068/install-canu-with-conda vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda/label/cf201901 canu Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/vik/anaconda3/envs/vikENV added / updated specs: - canu The following packages will be downloaded: package | build ---------------------------|----------------- canu-1.4 | 1 7.0 MB bioconda/label/cf201901 ------------------------------------------------------------ Total: 7.0 MB The following packages will be SUPERSEDED by a higher-priority channel: canu bioconda --> bioconda/label/cf201901 Proceed ([y]/n)? y Downloading and Extracting Packages canu-1.4 | 7.0 MB | ################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> LEGE https://bioinformaticsonline.com/snippets/view/42909/perl-script-to-get-all-the-descendent-in-a-tree Tue, 23 Feb 2021 11:56:59 -0600 https://bioinformaticsonline.com/snippets/view/42909/perl-script-to-get-all-the-descendent-in-a-tree use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile', -directory=> "taxdump", -nodesfile=> "taxdump/nodes.dmp", -namesfile=> "taxdump/names.dmp"); my $taxon = $dbh->get_taxon(-taxonid => 10190); my @taxa = $dbh->get_all_Descendents($taxon); foreach (@taxa) {print $_->id; print "\n";}]]> LEGE