Select CDS by keyword in all E. coli genomes

gistfile1.sh

#!/bin/bash

query=$1

genome_ids=$(wget -qO - "http://www.ncbi.nlm.nih.gov/genome/genomes/167?&subset=complete&limit=refseq" | grep 'title="chromosome">Chr' | sed -E 's/.+(NC_.+|NZ_.+)/\1/' | cut -d \< -f 1)

for genome_id in $genome_ids
do
   wget -qO - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$genome_id&rettype=gb&retmode=xml" > genome.xml
   gene_ids=$(xmllint --xpath "//GBFeature[GBFeature_key[.='CDS'] and GBFeature_quals/GBQualifier[GBQualifier_name[.='product'] and GBQualifier_value[contains(.,\"$query\")]]]" genome.xml | grep "GI:" | sed -E 's/.+GI:(.+)<.+/\1/')
   for gene_id in $gene_ids
   do
       wget -qO - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$gene_id&rettype=fasta" | grep "^>" | cut -d \> -f 2
   done
done

rm genome.xml