ncbi-one-liners

A collection of NCBI one-liners

Example input

SAMPLE=PNUSAC017705

Get SRR identifiers from sample names

    echo $SAMPLE | \
      esearch -db biosample -query $SAMPLE | \
      elink --target sra | \
      efetch -format xml | \
      xtract -pattern EXPERIMENT_PACKAGE -element SAMPLE@alias -element RUN@accession -block DESIGN | \
      awk -v ID="$SAMPLE" '{print ID"\t"$0}';