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#!/bin/sh
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information (NCBI)
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government do not place any restriction on its use or reproduction.
# We would, however, appreciate having the NCBI and the author cited in
# any work or product based on this material.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# ===========================================================================
#
# File Name: bt-srch
#
# Author: Jonathan Kans
#
# Version Creation Date: 2/6/19
#
# ==========================================================================
# Front-end for expanding Entrez Direct style of command-line navigation to
# external resources maintained by BioThings.io. See comments in xplore
# script for credits and references.
debug=false
if [ "$#" -gt 1 ]
then
if [ "$1" = "-debug" ]
then
debug=true
shift
fi
fi
if [ "$#" -lt 1 ]
then
echo "Must supply target argument"
exit 1
fi
dst="$1"
shift
que=""
tax=""
act=""
while [ $# -gt 0 ]
do
case "$1" in
-q | -query )
que=$2
shift
shift
;;
-organism | -taxname )
tax=$2
shift
shift
;;
-action | -actions )
act=$2
shift
shift
;;
-* )
exec >&2
echo "$0: Unrecognized option $1"
exit 1
;;
* )
break
;;
esac
done
case "$tax" in
human )
tax="9606"
;;
mouse )
tax="10090"
;;
rat )
tax="10116"
;;
fruitfly )
tax="7227"
;;
* )
break
;;
esac
case "$tax" in
*[^0-9]* ) # not a number (at least one non-digit somewhere)
tax=$(esearch -db taxonomy -query "$tax [SCIN]" | efetch -format uid)
;;
* ) # a number (all digits)
break
;;
esac
DoWrap() {
echo "<opt>"
sort -V | uniq -i |
while read uid
do
echo "<Id>$uid</Id>"
done
echo "</opt>"
}
DoLoad() {
xtract -wrp ENTREZ_EXTEND -pattern opt -wrp Type -lbl "$dst" \
-wrp Count -num Id -wrp Id -encode Id |
xtract -format
}
DoSearch() {
url="$1"
if [ -z "$que" ]
then
echo "Must supply -query argument"
exit 1
fi
if [ "$tax" != "" ]
then
que=$(echo "$que AND taxid:$tax")
fi
if [ "$act" != "" ]
then
que=$(echo "$que AND drugbank.targets.actions:$act")
fi
if [ "$debug" = true ]
then
echo "nquire -get $url query -q '$que' -fetch_all TRUE | xtract -j2x |" > /dev/tty
echo "xtract -pattern hits -element _id" > /dev/tty
fi
res=$(nquire -get "$url" query -q "$que" -fetch_all TRUE | xtract -j2x)
sid=$(echo "$res" | xtract -pattern opt -element _scroll_id)
ttl=$(echo "$res" | xtract -pattern opt -element total)
while :
do
ids=$(echo "$res" | xtract -pattern hits -element _id)
echo "$ids"
nid=$(echo "$ids" | wc -l)
ttl=$((ttl - nid))
if [ $ttl -lt 1 ]
then
break
fi
res=$(nquire -get "$url" query -scroll_id "$sid" | xtract -j2x)
done
}
case "$dst" in
ncbigene )
DoSearch "http://mygene.info/v3" |
DoWrap |
DoLoad
break
;;
hgvs )
DoSearch "http://myvariant.info/v1" |
DoWrap |
xtract -wrp ENTREZ_EXTEND -pattern opt -wrp Type -lbl hgvs \
-wrp Count -num Id -wrp Id -encode Id |
xtract -format
break
;;
inchikey )
DoSearch "http://mychem.info/v1" |
DoWrap |
DoLoad
break
;;
* )
exec >&2
echo "$0: Unrecognized target $dst"
exit 1
;;
esac
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