I have a GenBank file (reference genome) and need to convert it to a corresponding embl file. I have no idea how to do this. I have tried to use EMBOSS-SEQRET (online tool), but I get an error saying that the GenBank file exceeded the size limit.
$ python -c "import sys; from Bio import SeqIO; SeqIO.convert(sys.stdin, 'embl', sys.stdout, 'genbank');" < infile.embl
# Append > outfile.gbk if you want to write to a file.
You will, of course, need BioPython. I suggest installing it via anaconda.
Example input:
ID AB000263 standard; RNA; PRI; 368 BP.
XX
AC AB000263;
XX
DE Homo sapiens mRNA for prepro cortistatin like peptide, complete cds.
XX
SQ Sequence 368 BP;
acaagatgcc attgtccccc ggcctcctgc tgctgctgct ctccggggcc acggccaccg 60
ctgccctgcc cctggagggt ggccccaccg gccgagacag cgagcatatg caggaagcgg 120
caggaataag gaaaagcagc ctcctgactt tcctcgcttg gtggtttgag tggacctccc 180
aggccagtgc cgggcccctc ataggagagg aagctcggga ggtggccagg cggcaggaag 240
gcgcaccccc ccagcaatcc gcgcgccggg acagaatgcc ctgcaggaac ttcttctgga 300
agaccttctc ctcctgcaaa taaaacctca cccatgaatg ctcacgcaag tttaattaca 360
gacctgaa 368
//
Example output:
LOCUS AB000263 368 bp RNA PRI 01-JAN-1980
DEFINITION Homo sapiens mRNA for prepro cortistatin like peptide, complete
cds..
ACCESSION AB000263
VERSION AB000263
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
ORIGIN
1 acaagatgcc attgtccccc ggcctcctgc tgctgctgct ctccggggcc acggccaccg
61 ctgccctgcc cctggagggt ggccccaccg gccgagacag cgagcatatg caggaagcgg
121 caggaataag gaaaagcagc ctcctgactt tcctcgcttg gtggtttgag tggacctccc
181 aggccagtgc cgggcccctc ataggagagg aagctcggga ggtggccagg cggcaggaag
241 gcgcaccccc ccagcaatcc gcgcgccggg acagaatgcc ctgcaggaac ttcttctgga
301 agaccttctc ctcctgcaaa taaaacctca cccatgaatg ctcacgcaag tttaattaca
361 gacctgaa
//
You can use the same tool on the command line. You will need to download and install EMBOSS package if you don't have it locally available.