type_strains.sh.in

#!/bin/bash

# Arguments: none

# Please crash on first mistake.
set -o pipefail -e

ENTREZ_URL=<<<ENTREZ_URL>>> 
ENTREZ_BATCH_SIZE=<<<ENTREZ_BATCH_SIZE>>>

tempfile="$(<<<CMD_MKTEMP>>> tmp.XXXXXXXX)"
> "$tempfile"

header="$(curl -d 'db=assembly'                       \
               -d 'term="sequence from type"'         \
               -d 'field=filter'                      \
               -d 'usehistory=y'                      \
               "$ENTREZ_URL/esearch.fcgi"             \
        | grep -e 'QueryKey' -e 'WebEnv' | tr -d '\n' \
        )"

query_key="$(echo "$header"                                             \
           | <<<CMD_SED>>> -n 's/.*<QueryKey>\(.*\)<\/QueryKey>.*/\1/p' \
           )"

web_env="$(echo "$header"                                         \
         | <<<CMD_SED>>> -n 's/.*<WebEnv>\(.*\)<\/WebEnv>.*/\1/p' \
         )"

returned="$ENTREZ_BATCH_SIZE"
retstart='1'
while ((returned == ENTREZ_BATCH_SIZE)); do
    returned="$(curl -d 'db=assembly'                                 \
                     -d "query_key=$query_key"                        \
                     -d "WebEnv=$web_env"                             \
                     -d "retmax=$ENTREZ_BATCH_SIZE"                   \
                     -d "retstart=$retstart"                          \
                     "$ENTREZ_URL/esummary.fcgi"                      \
              | grep '<Genbank>'                                      \
              | <<<CMD_SED>>> -e 's/<[^>]*>//g' -e 's/[ \t][ \t]*//g' \
              | tee -a "$tempfile"                                    \
              | wc -l                                                 \
              )"
    retstart="$((retstart + returned))"
done

# write out the type strain assembly ids sorted
<<<CMD_SORT>>> "$tempfile"

rm "$tempfile"