#!/bin/bash
while read line
do
id=$line
set +x
a=$(curl https://www.ncbi.nlm.nih.gov/biosample/`curl "https://www.ncbi.nlm.nih.gov/sra/?term=$id"|grep SAM|sed 's/SAM/\nSAM/g;'|sed 's/".*//; s/<.*//; s/ .*//'|grep "^SAM"|awk 'NR==1{print $0}'`)
set +o pipefail
lat="$id"$'\t'`echo "$a"|grep -i latitude|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 lat|tail -n 1`$'\t'`echo "$a"|
grep -i "collection date"|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 -i "collection date"|tail -n 1`
long="$id"$'\t'`echo "$a"|grep -i longitude|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 long|tail -n 1`$'\t'`echo "$a"|
grep -i "collection date"|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 -i "collection date"|tail -n 1`
str=$lat
latitude=(`echo $lat`)
longitude=(`echo $long`)
if [[ $lat == $long ]]; then
:
else
if [ `echo "${latitude[1]} > 0.0" | bc` == 1 ]; then
${latitude[1]}=${latitude[1]}" N"
else
${latitude[1]}=`echo ${latitude[1]}| sed 's/^-//'`" S"
fi
if [ `echo "${longitude[1]} > 0.0" | bc` == 1 ]; then
${longitude[1]}=${longitude[1]}" E"
else
${longitude[1]}=`echo ${longitude[1]}| sed 's/^-//'`" W"
fi
str=`echo -e ${latitude[0]}'\t'${latitude[1]}" "${longitude[1]}'\t'${latitude[2]}`
fi
set -x
echo -e "$str"
done