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Install gffread using Conda !
By Jit 1406 days ago
#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/
