Let's say, I have two accession numbers AP017458 & GQ994935 of a virus's GenBank file. I want to download the nucleotide sequence (CDS) of ORF57 from these accession from Linux terminal. As per as I know efetch, esearch, etc command line code can be used to download sequence directly from the terminal. But, I need only the coding sequence of a specific ORF.
How can I download the coding sequence of a specific ORF by using accession number (all together or, at least one accession per each run)?
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written
by
Anisur Rahman •
Using EntrezDirect (sequence truncated for space) :
$ esearch -db nuccore -query "AP017458" | elink -target protein | esummary | xtract -pattern DocumentSummary -if Title -contains "ORF57" -element Extra | awk -F "|" '{print $4}' | xargs -n 1 sh -c 'efetch -db protein -id $0 -format fasta_cds_na'
>lcl|AP017458.1_cds_BAV17910.1_1 [protein=ORF57] [protein_id=BAV17910.1] [location=join(82084..82131,82240..83559)] [gbkey=CDS]
ATGGTACAAGCAATGATAGACATGGACATTATGAAGGGCATCCTAGAGGACTCTGTGTCCTCCTCTGAGT
TTGACGAATCGAGGGACGACGAGACGGACGCACCGACACTGGAAGACGAGCAATTGTCCGAACCCGCCGA
GCCTCCGGCAGACGAGCGCATGCGTGGTACCCAGTCGGCCCAGGGAATCCCACCCCCCCTGGGCCGCATC
There are two entries for the other accession
$ esearch -db nuccore -query "GQ994935" | elink -target protein | esummary | xtract -pattern DocumentSummary -if Title -contains "ORF57" -element Extra | awk -F "|" '{print $4}' | xargs -n 1 sh -c 'efetch -db protein -id $0 -format fasta_cds_na'
>lcl|GQ994935.1_cds_ACY00456.1_1 [protein=ORF57] [protein_id=ACY00456.1] [location=join(81886..81934,82043..83361)] [gbkey=CDS]
ATGGTACAAGCAATGATAGACATGGACATTATGAAGGGCATCCTAGAGGACTCTGTGTCCTCCTCTGAGT
TTGACGAATCGAGGGACGACGAGACGGACGCACCGACACTGGAAGACGAGCAATTGTCCGAACCCGCCGA
>lcl|KF588566.1_cds_AKE33094.1_1 [gene=ORF57] [protein=ORF57] [protein_id=AKE33094.1] [location=join(81886..81934,82043..83361)] [gbkey=CDS]
ATGGTACAAGCAATGATAGACATGGACATTATGAAGGGCATCCTAGAGGACTCTGTGTCCTCCTCTGAGT
TTGACGAATCGAGGGACGACGAGACGGACGCACCGACACTGGAAGACGAGCAATTGTCCGAACCCGCCGA
GCCTCCGGCAGACGAGCGCATCCGTGGTACCCAGTCGGCCCAGGGAATCCCACCCCCCCTGGGCCGCATC
Hi, your code is just amazing. Thank you very much. Is it possible to download the CDS from more than one accession together in a single code? Becuase I have a very long list of accession numbers and I've to download CDS of ORF57 for all of them.
Absolutely. Use epost method :
$ epost -db nuccore -input id_file | elink -target protein | esummary | xtract -pattern DocumentSummary -if Title -contains "ORF57" -element Extra | awk -F "|" '{print $4}' | xargs -n 1 sh -c 'efetch -db protein -id $0 -format fasta_cds_na'
id_file should contain one accession per line.
You made my day. Thank you very much.
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