Added sampling script

sample_srr

@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+import urllib.request
+import zlib
+from ftplib import FTP
+import sys
+
+def main():
+    # SRR12478073 is a good test
+    accession,skip,sample = sys.argv[1:]
+    url = get_url(accession)
+
+    sample_url(url,int(skip),int(sample))
+
+
+def sample_url(url,skip,sample):
+    url_sections = url.split("/")
+    server = url_sections[0]
+    file = url_sections[-1]
+    folder = "/".join(url_sections[1:-1])
+
+    decompressor = collect_gzip_data(skip,sample)
+
+    #print(f"URL is {url} server={server} folder={folder} file={file}")
+
+    #print(f"Connecting to {server}")
+    ftp = FTP(server)
+    #print(f"Logging in")
+    ftp.login()
+    #print(f"Moving to {folder}")
+    ftp.cwd(folder)
+    ftp.retrbinary("RETR "+file,decompressor, blocksize=124)
+
+    ftp.quit()
+
+
+def collect_gzip_data(skip,collect):
+    decompressor = zlib.decompressobj(zlib.MAX_WBITS|16)
+    newline_count = 0
+
+    def accept_data(chunk):
+        nonlocal decompressor
+        nonlocal newline_count
+
+        new_data = decompressor.decompress(chunk).decode('utf-8')
+
+        lines = new_data.split("\n")
+
+        for i in range(len(lines)):
+            if newline_count >= 4*skip:
+                print(lines[i],end='')
+                if i < len(lines)-1:
+                    print("\n",end='')
+
+            if i < len(lines)-1:
+                newline_count += 1
+
+            if newline_count >= 4*(skip+collect):
+                sys.exit()
+
+    return(accept_data)
+
+def get_url(accession):
+    # Get the FTP locations for the sample
+    ena_rest_url = f"https://www.ebi.ac.uk/ena/portal/api/filereport?accession={accession}&result=read_run&fields=run_accession,fastq_ftp"
+
+
+    with urllib.request.urlopen(ena_rest_url) as response:
+        if response.getcode() != 200:
+            raise IOError(f"[ENA] Got error code {response.getcode()} from ENA REST for accession {sample['accession']}")
+
+        url = ""
+
+        found_accession_line = False
+
+        for line in response:
+            line = line.decode("UTF-8").strip()
+            #print(line)
+            if line.startswith("SRR"):
+                found_accession_line = True
+                sections = line.split("\t")
+
+                if len(sections) != 2:
+                    raise IOError(f"[ENA] No ENA fastq files found for accession {sample['accession']}")
+
+                url = sections[1].split(";")[0] # Just take the first read if there are multiple available
+                return(url)
+
+        raise IOError(f"[ENA] Found no accession in response from ENA REST for accession {sample['accession']}")
+
+
+
+if __name__ == "__main__":
+    main()