--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/retrieve.py	Mon Jan 22 16:41:50 2018 -0500
@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+
+# NCBI SRA Tools
+# https://galaxyproject.org/tutorials/upload/
+
+import os
+import optparse
+from subprocess import Popen, PIPE
+
+db_key = "?";
+sra_instant_url = "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/";
+
+def convertSRA(tmp_dir, accession_number, data_format):
+    absolute_tmp_dir = os.path.abspath(tmp_dir);
+    sra_file_path = os.path.join(absolute_tmp_dir, accession_number+".sra");
+    if os.path.isdir(absolute_tmp_dir) and os.path.exists(sra_file_path):
+        process = None;
+        if data_format == ".fasta.gz":
+            process = Popen(["fastq-dump", "--fasta", "--gzip", sra_file_path, "--outdir", absolute_tmp_dir], stdout=PIPE);
+        elif data_format == ".fastq.gz":
+            process = Popen(["fastq-dump", "--gzip", sra_file_path, "--outdir", absolute_tmp_dir], stdout=PIPE);
+        elif data_format == ".fasta":
+            process = Popen(["fastq-dump", "--fasta", sra_file_path, "--outdir", absolute_tmp_dir], stdout=PIPE);
+        elif data_format == ".fastq":
+            process = Popen(["fastq-dump", sra_file_path, "--outdir", absolute_tmp_dir], stdout=PIPE);
+        else:
+            process = None;
+        if process is not None:
+            (output, err) = process.communicate();
+            if err:
+                # kill the process
+                # kill_process(process.pid);
+                # remove any trace of the output file
+                an_file_path = os.path.join(tmp_dir, accession_number+data_format);
+                if os.path.exists(an_file_path):
+                    os.unlink(an_file_path);
+                # try to restart the process
+                return downloadAccessionData(tmp_dir, accession_number, data_format);
+            #exit_code = process.wait();
+            return os.path.join(tmp_dir, accession_number+data_format);
+    return "";
+
+def downloadAccessionData(accession_number, accession_path, appdata_path, data_format, limit=10):
+    split = accession_number[:6];
+    srr_path = sra_instant_url+split+"/"+accession_number+"/"+accession_number+".sra";
+    sra_file_path = os.path.join(appdata_path, accession_number+".sra");
+    process = Popen(['wget', srr_path, "--output-document="+sra_file_path], stdout=PIPE);
+    (output, err) = process.communicate();
+    if err:
+        # remove any trace of the output file
+        if os.path.exists(an_file_path):
+            os.unlink(an_file_path);
+        # try to restart the process
+        if limit > 0:
+            return downloadAccessionData(accession_number, accession_path, appdata_path, data_format, limit-1);
+        return -1;
+    if os.path.exists(sra_file_path):
+        converted_file_path = convertSRA(appdata_path, accession_number, data_format);
+        if os.path.exists(converted_file_path):
+            os.rename(converted_file_path, accession_path);
+        os.unlink(sra_file_path);
+    return 0;
+
+def process_accessions( options, args ):
+    # create appdata dir if it does not exist
+    appdata_path = options.appdata;
+    if not os.path.exists(appdata_path):
+        os.makedirs(appdata_path);
+    data_format = options.dataformat;
+    '''
+    # Collection test
+    test_file_name = "Test Collection" + "_" + "SRRtest" + "_" + data_format[1:] + "_" + db_key;
+    test_file_path = os.path.join(appdata_path, test_file_name);
+    file = open(test_file_path, "w");
+    file.write("Hello World");
+    file.close();
+    '''
+    # read inputs
+    comma_sep_file_paths = options.files;
+    #print("files: "+str(comma_sep_file_paths)+" - "+str(type(comma_sep_file_paths)));
+    # check if options.files contains at least one file path
+    if comma_sep_file_paths is not None:
+        # split file paths
+        file_paths = comma_sep_file_paths.split(",");
+        # split file names
+        comma_sep_file_names = str(options.names);
+        #print("names: "+str(comma_sep_file_names));
+        file_names = comma_sep_file_names.split(",");
+        # populate a dictionary with the files containing the sequences to query
+        for idx, file_path in enumerate(file_paths):
+            file_name = file_names[idx];
+            #print(file_name + ": " + file_path);
+            with open(file_path) as accessions:
+                for line in accessions:
+                    if line.strip() != "" and not line.startswith(">"):
+                        accession_number = line.strip();
+                        filename_with_collection_prefix = file_name + "_" + accession_number + "_" + data_format[1:] + "_" + db_key;
+                        accession_path = os.path.join(appdata_path, filename_with_collection_prefix)
+                        # download fastq filte related to accession_number
+                        downloadAccessionData( accession_number, accession_path, appdata_path, data_format );
+    return 0;
+
+def __main__():
+    # Parse the command line options
+    usage = "Usage: retrieve.py --files comma_sep_file_paths --names comma_seq_file_names --format data_format --appdata folder_name";
+    parser = optparse.OptionParser(usage = usage);
+    parser.add_option("-f", "--files", type="string",
+                    action="store", dest="files", help="comma separated files path");
+    parser.add_option("-n", "--names", type="string",
+                    action="store", dest="names", help="comma separated names associated to the files specified in --files");
+    parser.add_option("-e", "--format", type="string",
+                    action="store", dest="dataformat", help="data format");
+    parser.add_option("-a", "--appdata", type="string",
+                    action="store", dest="appdata", help="appdata folder name");
+    parser.add_option("-v", "--version", action="store_true", dest="version",
+                    default=False, help="display version and exit");
+    (options, args) = parser.parse_args();
+    if options.version:
+        print __version__;
+    else:
+        return process_accessions( options, args );
+
+if __name__ == "__main__": __main__()