Hi, I have a protein IntelliGenetics file used in the Biopython test suite: http://biopython.org/SRC/biopython/Tests/IntelliGenetics/VIF_mase-pro.txt
I am using EMBOSS 6.1.0 (patch level 2 I think), and I am trying to turn this into a "GenBank Protein File", or GenPept file, using EMBOSS seqret. EMBOSS can read the file fine, this works: $ seqret -auto -sformat=ig -osformat=fasta VIF_mase-pro.txt temp.txt Giving FASTA output with 16 gapped protein sequences, which is good - although the ID of the first record is a bit odd. Using "genbank" as the output format in EMBOSS seems to mean nucleotide and not protein: $ seqret -auto -sformat=ig -osformat=genbank VIF_mase-pro.txt temp.txt Error: Sequence format 'genbank' not supported for protein sequences Error: Sequence format 'genbank' not supported for protein sequences ... Error: Sequence format 'genbank' not supported for protein sequences Referring to the documentation, http://emboss.sourceforge.net/docs/themes/SequenceFormats.html I then tried "genpept" and "refseqp": $ seqret -auto -sformat=ig -osformat=genpept VIF_mase-pro.txt temp.txt Error: Unknown output format 'genpept' Error: Unknown output format 'genpept' ... Error: unknown output format 'genpept' $ seqret -auto -sformat=ig -osformat=refseqp VIF_mase-pro.txt temp.txt Error: Unknown output format 'refseqp' Error: Unknown output format 'refseqp' ... Error: unknown output format 'refseqp' Doesn't EMBOSS seqret support genpept/refseqp as an output format? Thanks, Peter C. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
