E-utilities for obtain gene sequences from the gene database

Question

[dllopezr]

Hi everyone

I need to download all gene sequences from a query gene in gene ncbi database through e-utilites in linux command line. The next command (adapted from ncbi example) works for gene to protein:

esearch -db gene -query "nifH AND Sinorhizobium meliloti 1021 [orgn]" | elink -target protein -name gene_protein_refseq | efetch -format fasta

But when I try this:

esearch -db gene -query "nifH AND Sinorhizobium meliloti 1021 [orgn]" | elink -target nuccore -name gene_nuccore_refseqgene | efetch -format fasta

I obtain this error msg:

QueryKey value not found in fetch input

As a note: ncbi examples of how to do this search don't exist, so I am question myself if it is possible to conect gene db with nucleotide db, of retrieve gene sequences from gene database as well

Thank you for your suggestions

Answer 1

[GenoMax]

Extending query you were trying:

esearch -db gene -query "nifH AND Sinorhizobium meliloti 1021 [orgn]" | efetch -format docsum | xtract -pattern GenomicInfoType -element ChrAccVer -element ChrStart -element ChrStop |xargs -n 3 sh -c 'efetch -db nuccore -id "$0" -seq_start "$1" -seq_stop "$2" -format fasta'

Should get you

>NC_003037.1:453555-454448 Sinorhizobium meliloti 1021 plasmid pSymA, complete sequence
GATGGCAGCTCTGCGTCAGATCGCGTTCTACGGTAAGGGGGGTATCGGCAAGTCCACGACCTCCCAAAAT
ACACTCGCCGCGCTTGTCGACCTGGGGCAAAAGATCCTTATTGTCGGCTGCGATCCGAAAGCGGACTCCA
CGCGCCTCATCCTGAACGCAAAGGCACAGGACACCGTACTGCATCTTGCGGCAACCGAAGGTTCGGTCGA
AGACCTCGAGCTCGAGGACGTGCTCAAAGTGGGTTACAGAGGCATCAAGTGCGTGGAGTCCGGTGGCCCA
GAGCCGGGCGTCGGCTGCGCCGGACGCGGCGTTATCACCTCGATCAACTTCCTGGAAGAGAACGGCGCTT
ACAACGATGTCGATTACGTCTCATACGACGTGCTAGGGGACGTAGTATGCGGCGGCTTTGCGATGCCTAT
TCGCGAAAACAAGGCTCAGGAAATCTACATCGTCATGTCCGGTGAGATGATGGCGCTCTATGCCGCCAAC
AACATCGCGAAGGGTATCCTGAAGTACGCCCATGCGGGCGGCGTGCGGCTGGGGGGGTTGATTTGCAACG
AGCGCCAGACCGATCGGGAGCTCGACCTCGCCGAGGCACTTGCCGCCCGCCTCAATTCCAAGCTCATCCA
CTTCGTGCCGCGCGACAATATCGTTCAGCACGCAGAGCTCAGAAAGATGACAGTGATCCAATATGCGCCG
AACTCTAAGCAAGCCGGGGAATATCGCGCCCTGGCTGAAAAGATCCATGCAAATTCCGGCCGAGGCACCG
TCCCTACACCGATCACTATGGAGGAACTGGAGGACATGCTGCTCGACTTTGGAATCATGAAGAGCGACGA
GCAGATGCTTGCCGAACTCCACGCCAAGGAAGCCAAGGTAATAGCCCCCCACTG