技巧 | 从 GFF 文件提取 CDS 并翻译成蛋白

Usage:
gffread  [-g  | ][-s ] 
 [-o ] [-t ] [-r [[]:].. [-R]]
 [-CTVNJMKQAFGUBHZWTOLE] [-w ] [-x ] [-y ]
 [-i ] 
 Filters and/or converts GFF3/GTF2 records.
  is a GFF file, use '-' if the GFF records will be given at stdin
 
 Options:
  -g  full path to a multi-fasta file with the genomic sequences
      for all input mappings, OR a directory with single-fasta files
      (one per genomic sequence, with file names matching sequence names)
  -s   is a tab-delimited file providing this info
      for each of the mapped sequences:
        
      (useful for -A option with mRNA/EST/protein mappings)
  -i  discard transcripts having an intron larger than 
  -r  only show transcripts overlapping coordinate range ..
      (on chromosome/contig , strand  if provided)
  -R  for -r option, discard all transcripts that are not fully 
      contained within the given range
  -U  discard single-exon transcripts
  -C  coding only: discard mRNAs that have no CDS feature
  -F  full GFF attribute preservation (all attributes are shown)
  -G  only parse additional exon attributes from the first exon
      and move them to the mRNA level (useful for GTF input)
  -A  use the description field from  and add it
      as the value for a 'descr' attribute to the GFF record
  
  -O  process also non-transcript GFF records (by default non-transcript
      records are ignored)
  -V  discard any mRNAs with CDS having in-frame stop codons
  -H  for -V option, check and adjust the starting CDS phase
      if the original phase leads to a translation with an 
      in-frame stop codon
  -B  for -V option, single-exon transcripts are also checked on the
      opposite strand
  -N  discard multi-exon mRNAs that have any intron with a non-canonical
      splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
  -J  discard any mRNAs that either lack initial START codon
      or the terminal STOP codon, or have an in-frame stop codon
      (only print mRNAs with a fulll, valid CDS)
  --no-pseudo: filter out records matching the 'pseudo' keyword
 
  -M/--merge : cluster the input transcripts into loci, collapsing matching
       transcripts (those with the same exact introns and fully contained)
  -d  : for -M option, write collapsing info to file 
  --cluster-only: same as --merge but without collapsing matching transcripts
  -K  for -M option: also collapse shorter, fully contained transcripts
      with fewer introns than the container
  -Q  for -M option, remove the containment restriction:
      (multi-exon transcripts will be collapsed if just their introns match,
      while single-exon transcripts can partially overlap (80%))
 
  --force-exons: make sure that the lowest level GFF features are printed as 
      "exon" features
  -E  expose (warn about) duplicate transcript IDs and other potential 
      problems with the given GFF/GTF records
  -D  decode url encoded characters within attributes
  -Z  merge close exons into a single exon (for intron size<4)
  -w  write a fasta file with spliced exons for each GFF transcript
  -x  write a fasta file with spliced CDS for each GFF transcript
  -W  for -w and -x options, also write for each fasta record the exon
      coordinates projected onto the spliced sequence
  -y  write a protein fasta file with the translation of CDS for each record
  -L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
  -m   is a reference (genomic) sequence replacement table with
      this format:
       
      GFF records on reference sequences that are not found among the
       entries in this file will be filtered out
  -o  the "filtered" GFF records will be written to 
      (use -o- for printing to stdout)
  -t  use  in the second column of each GFF output line
  -T  -o option will output GTF format instead of GFF3

$ conda install gffread
$ gffread test.gff3 -g genome.fa -x cds.fa -y protein.fa

Ref | 根据基因组 fa 文件和 gff 文件提取 cds 并翻译成 pep