EMBL-EBI Web Services

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====== cURL ======

  * [[http://curl.haxx.se/]]

Fetching database entries using a basic POST request to [[http://www.ebi.ac.uk/Tools/dbfetch|dbfetch]]:
<code bash>
#!/bin/sh
url='http://www.ebi.ac.uk/Tools/dbfetch/dbfetch'
curl --silent --data 'db=uniprot' --data 'id=WAP_RAT,WAP_MOUSE' --data 'format=default' --data 'style=raw' "$url"
</code>

Submitting a job to [[:services:sss:NCBI BLAST (REST)]] using a database entry identifier for the query sequence:
<code bash>
#!/bin/sh

baseUrl='http://www.ebi.ac.uk/Tools/services/rest/ncbiblast'

# Submit job.
url="$baseUrl/run"
email='support@ebi.ac.uk'
jobId=`curl -s -d "email=$email" \
-d 'stype=protein' \
-d 'program=blastp' \
-d 'database=uniprotkb_swissprot' \
-d 'sequence=UNIPROT:WAP_RAT' \
$url`
echo "JobId: $jobId"

# Job status polling.
url="$baseUrl/status/$jobId"
status='PENDING'
while [ "$status" = 'PENDING' -o "$status" = 'RUNNING' ]; do
    sleep 3
    status=`curl -s "$url"`
    echo "$status"
done

# Get available result types.
url="$baseUrl/resulttypes/$jobId"
resultTypeXml=`curl -s "$url"`
resultTypeList=`echo "$resultTypeXml" | xpath -e '//identifier' 2> /dev/null | sed 's#<[^>]*>##g'`

# Get results.
for resultType in $resultTypeList; do
    url="$baseUrl/result/$jobId/$resultType"
    curl -s "$url"
done
</code>

Submitting a job to [[:services:msa:MUSCLE (REST)]] using input data from a file:
<code bash>
#!/bin/sh

baseUrl='http://www.ebi.ac.uk/Tools/services/rest/muscle'

# Submit job.
url="$baseUrl/run"
email='support@ebi.ac.uk'
jobId=`curl -s -d "email=$email" \
--data-urlencode "sequence@$HOME/test/data/sequence/prot_test_multi_1433.tfa" \
$url`
echo "JobId: $jobId"

# Job status polling.
url="$baseUrl/status/$jobId"
status='PENDING'
while [ "$status" = 'PENDING' -o "$status" = 'RUNNING' ]; do
    sleep 3
    status=`curl -s "$url"`
    echo "$status"
done

# Get available result types.
url="$baseUrl/resulttypes/$jobId"
resultTypeXml=`curl -s "$url"`
resultTypeList=`echo "$resultTypeXml" | xpath -e '//identifier' 2> /dev/null | sed 's#<[^>]*>##g'`

# Get results.
for resultType in $resultTypeList; do
    url="$baseUrl/result/$jobId/$resultType"
    curl -s "$url"
done
</code>
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