When I load a multi-record genbank file into Artemis, it opens only the first contig. Are there any tools to concatenate a multi-record genbank file into a single record genbank file?
You use EMBOSS union like this:
% union -sequence in.gbk -outseq out.gbk -osformat genbank -feature -auto
You can view this in Artemis
% art out.gbk
Hi Pieter, You can try Geneious. Free and pretty powerful suite of software.
http://www.geneious.com
I believe Artemis needs a single Genbank record, so it ignores all the rest after the first. The EMBOSS command/utility called 'union' will concatenate Genbank files. Be sure to use the '-features Y' option to force it to include the features from all the files in the output; by default it won't. One caveat - I've used this for concatenating multiple files. Not sure what it does with a multi-record file.
It is also possible to programmatically read in the multi-record Genbank file using BioPython (or BioPerl) and then join all the records into 1 and output that as a single Genbank file.
Geneious doesn't seem to be free.
EMBOSS-union also only reads the first contig.
Does anyone has a working Python script to concatenate multiple records in a genbank file?
indentation will be off (used dots for indents), so will need to fix it, but this should work:
from Bio import SeqIO
merged_rec = ''
infile = "multi-rec.gbk"
for rec in SeqIO.parse(open(infile,"r"), "genbank") :
....merged_rec += rec
....# you could insert a spacer if needed
....# merged_rec += rec + ("N" * 50)
merged_rec.id = "mergedseq"
merged_rec.description = "merged seq"
SeqIO.write(merged_rec, "merged.gbk", "genbank")
You use EMBOSS union like this:
% union -sequence in.gbk -outseq out.gbk -osformat genbank -feature -auto
You can view this in Artemis
% art out.gbk
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