https://bioinformaticsonline.com/snippets/view/42638/install-gffread-using-conda? https://bioinformaticsonline.com/snippets/view/42638/install-gffread-using-conda Sun, 17 Jan 2021 00:37:14 -0600 https://bioinformaticsonline.com/snippets/view/42638/install-gffread-using-conda #GffRead: GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. https://github.com/gpertea/gffread (jitENV) jitendra@Bathymodiolus:~$ conda install -c bioconda gffread Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/jitendra/.conda/envs/jitENV added / updated specs: - gffread The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | main 3 KB gffread-0.12.1 | h8b12597_0 635 KB bioconda libgcc-ng-9.1.0 | hdf63c60_0 5.1 MB libstdcxx-ng-9.1.0 | hdf63c60_0 3.1 MB zlib-1.2.11 | h7b6447c_3 103 KB ------------------------------------------------------------ Total: 8.9 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main gffread bioconda/linux-64::gffread-0.12.1-h8b12597_0 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 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Proceed ([y]/n)? y Downloading and Extracting Packages zlib-1.2.11 | 103 KB | ##################################### | 100% _libgcc_mutex-0.1 | 3 KB | ##################################### | 100% libstdcxx-ng-9.1.0 | 3.1 MB | ##################################### | 100% libgcc-ng-9.1.0 | 5.1 MB | ##################################### | 100% gffread-0.12.1 | 635 KB | ##################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done #Run as follows (jitENV) jitendra@Bathymodiolus:~$ gffread -w cds.fa -g ed.clean.fasta gene_structures_post_PASA_updates.19157.gff3 #There are also another good option python gff2fa.py -t CDS ../../GCF_0355.2_L0_genomic.gff ../../GCF_001039355.2_L0_genomic.fna > La.cds.fa #Find more at http://blog.shenwei.me/extract-cds-fastas-from-a-gff-annotation-reference-sequence/]]> Jit