Adding EBI pulldown script

scripts/get_new_samples_EBI.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+# Grab any sample accessions that do not exist
+
+study_accession=ERP012803
+count=-1
+
+# Grab all the secondary sample accession numbers and file links from EBI
+curl -s "http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=${study_accession}&result=read_run&fields=secondary_sample_accession,submitted_ftp" | grep -v "^secondary_sample_accession" > ${study_accession}.details.txt
+
+# Each line of the file `${study_accession}.details.txt` contains the secondary
+# sample accession followed by the link to download the file
+# This `awk` command splits such line in 2
+for fq in `awk '{print $1, $2}' ${study_accession}.details.txt`
+do
+    ((count++))
+    if [[ $(( count % 2)) -eq 0 ]]
+    then
+        # Even case, we have the secondary sample accession number
+        id=$fq
+        current_path=${study_accession}/${id}
+        current_base=${current_path}/${id}
+
+        # Check if we already have the metadata of the currrent sample
+        if [ -d "${current_path}" ]; then
+            continue
+        fi
+        echo "Fetching ${id}..."
+
+        # Retrieving the sample metadata
+        mkdir -p ${current_path}
+        curl -s "http://www.ebi.ac.uk/ena/data/view/${id}&display=xml" > ${current_base}.txt &
+    else
+        # Odd case, we have the link to the sequence file
+        # Check if we already have the sequence file for the current sample,
+        # note that current_base gets defined in the previous iteration of the
+        # for loop
+        if [ -e "${current_base}.fna" ]; then
+            continue
+        fi
+
+        # Retrieve the FASTQ sequence file and transform it to FASTA
+        # sed from http://stackoverflow.com/a/10359425/19741
+        curl -s $fq | zcat | sed -n '1~4s/^@/>/p;2~4p' > ${current_base}.fna &
+    fi
+
+    # Only doing 10 downloads (5 samples) in parallel, so wait until the
+    # previous processes are done before continuing downloading data
+    if [[ $((count % 10)) -eq 0 ]]
+    then
+        wait
+    fi
+done
+
+# Wait until all downloads are completed
+wait