GenBank to fasta sequence

Question

[Kumar]

Hi,

I have a large file of Genbank format of nucleotide sequence, now I need fetch fasta sequence of all entries in file.

[Sishuo Wang]

from Bio import SeqIO
SeqIO.convert(infile_genbank, "genbank", outfile, "fasta")

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/genbank2fasta/

[venu]

You can use Sequence Manipulation Suite.

Answer 1

[Pierre Lindenbaum]

something like:

$ curl -Ls "ftp://ftp.ncbi.nlm.nih.gov/genbank/gbenv80.seq.gz" | gunzip -c |\
awk '/^ACCESSION   / {printf(">%s\n",$2);next;} /^ORIGIN/ {inseq=1;next;} /^\/\// {inseq=0;} {if(inseq==0) next; gsub(/[0-9 ]/,"",$0); printf("%s\n",$0);}' |\
head -n 30

>KP304532
cgcggcctatcagcttgttggtgaggtaatggctcaccaaggcaacgacgggtagctggt
ctgagaggacgatcagccacactggaactgagacacggtccagactcctacgggaggcag
cagcagggaatcttgcgcaatgggcgaaagcctgacgcagcgacgccgcgtgggggatga
aggccttcgggttgtaaacccctttcaggagggaagaaaatgacggtacctccagaagaa
gccccggccaactacgtgccagcagccgcggtaatacgtagggggcgagcgttgtccgga
tttattgggcgtaaagggctcgtaggcggcttgacaagtcgatcgtgaaaactcagggct
caaccctgagacgccggtcgatactgtcatggctagggtccggtagaggagaatggaatt
cccggtgtagcggtgaaatgcgcagatatcgggaggaacaccagtagcgaaggcggtcct
ctgggccggtaccgacgctgaggagcgaaagcgtggggagcaaacaggattagataccct
ggtagtccacgccgtaaacgttgggtactaggtgtggcgtctttatcaacggatgccgtg
ccgaagctaacgcattaagtaccccgcctggggagtacgg
>KP304533
cgcggcctatcagcttgttggtggggtaacggcctaccaaggcatcgacgggtagctggt
ctgagaggacgatcagccacactgggactgagacacggcccagactcctacgggaggcag
cagtggggaatattgcgcaatgggcgaaagcctgacgcagcaacgccgcgtgggggatga
aggctttcgggttgtaaacccctttcagtgatgacgaaaatgacggtaatcacagaagaa
gccccggccaactacgtgccagcagccgcggtaacacgtagggggcgagcgttgtccgga
tttattgggcgtaaagagctcgtaggcggttgcgtaagtcggacgtgaaaactcagggct
caaccctgagatgccgttcgatactgcgctgactagagtccggtaggggagcatggaatt
cctggtgtagcggtgaaatgcgcagatatcaggaggaacaccagtggcgaaggcggtgct
ctgggccggaactgacgctgaggagcgaaagcatgggtagcaaacaggattagataccct
ggtagtccatgccgtaaacgttgggcactaggtgtgggacctacttaacgggttccgtgc
cgtagctaacgcattaagtgccccgcctggggagtacgg
>KP304534
cgcggcctatcagcttgttggtgaggtaacggctcaccaaggcatcgacgggtagctggt
ctgagaggacgatcagccacactgggactgagacacggcccagactcctacgggaggcag
cagtagggaatcttgcgcaatgggcgaaagcctgacgcagcaacgccgcgtgggggatga
aggccttcgggtcgtaaacccctttcagcagggacgaaaatgacggtacctgcagaagaa
ggtccggccaactacgtgccagcagccgcggtaatacgtagggaccaagcgttgtccgga

Answer 2

[osullivanchristopher]

why not just use efetch?

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=KP304532&rettype=fasta

http://www.ncbi.nlm.nih.gov/books/NBK25499/

[soaresp2]

Because the use case is how to convert a large file into FASTA format, not how to get a sequence by accession number in Fasta format.