excel creator simplified

.gitignore

 java
 sra
+tmp

README.md

-# sra
+# sra to metadata excel file
 
-SRA XML crawler for datasets
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+SRA XML query and parser interface for datasets available through ENA.
+
+To use it you need to provide 3 arguments.
+
+For example:
+
+To generate the excel file for these three projects you can use the following argument:
+
+python3 study_creator.py "DRP005906|DRP007222|DRP007099" example@email.nl myexcelfilename.xlsx
+
+To only create an excel file for one project you can use:
+
+python3 study_creator.py "DRP005906" example@email.nl myexcelfilename.xlsx
+
+The first argument after calling the python script is based on the entrez query syntax so you can make more sophisticated queries using the advanced search engine at https://www.ebi.ac.uk/ena/browser/advanced-search.
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entrez.py

-import os
-import sys
-
-from Bio import Entrez
-from joblib import Parallel, delayed
-from joblib.externals.loky.process_executor import TerminatedWorkerError
-
-
-def processInput(identifier):
-    identifier = str(identifier)
-    folder = make_folder(identifier)
-    path = folder + "/" + identifier + ".xml"
-
-    if os.path.isfile(path):
-        # print("Already exists")
-        return path
-
-    Entrez.email = "ja@nee.com"
-
-    handle = Entrez.efetch(db="sra", id=identifier, rettype="xml", retmode="text")
-
-    content = handle.read()
-
-    print(path)
-    with open(path, 'w') as f:
-        print(content, file=f)
-
-    return path
-
-
-def make_folder(identifier):
-    folder = ""
-    # print(identifier)
-    for e in identifier:
-        if len(folder) % 4 == 0:
-            folder = folder + "/"
-        folder = folder + e
-    return "./sra" + folder
-
-
-while True:
-    query = "(((((\"paired\"[Layout]) AND ((\"instrument illumina hiseq 1000\"[Properties] OR \"instrument illumina hiseq 1500\"[Properties] OR \"instrument illumina hiseq 2000\"[Properties] OR \"instrument illumina hiseq 2500\"[Properties] OR \"instrument illumina hiseq 3000\"[Properties] OR \"instrument illumina hiseq 4000\"[Properties] OR \"instrument illumina hiseq x ten\"[Properties] OR \"instrument illumina miseq\"[Properties]))) AND \"illumina\"[Platform]) AND \"amplicon\"[Strategy]) AND \"filetype fastq\"[Properties]) AND \"cluster public\"[Properties]"
-    query = "PRJNA527973"
-    # query = "PRJNA517152"
-    Entrez.email = "A.N.Other@example.com"  # Always tell NCBI who you are
-    handle = Entrez.esearch(db="sra",
-                            term=query,
-                            # term="(("
-                            #      "("
-                            #      "\"paired\"[Layout] AND \"illumina\"[Platform]"
-                            #      ") AND \"strategy amplicon\"[Properties]"
-                            #      ") AND \"amplicon\"[Strategy] AND \"filetype fastq\"[Properties]"
-                            #      ") AND "
-                            #      "("
-                            #      "cluster_public[prop] AND \"filetype fastq\"[Properties]"
-                            #      ") AND "
-                            #      "("
-                            #      "(\""
-                            #      "instrument illumina hiseq 1000\"[Properties] OR \"instrument illumina hiseq 1500\"[Properties] OR \"instrument illumina hiseq 2000\"[Properties] OR \"instrument illumina hiseq 2500\"[Properties] OR \"instrument illumina hiseq 3000\"[Properties] OR \"instrument illumina hiseq 4000\"[Properties] OR \"instrument illumina hiseq x ten\"[Properties] OR \"instrument illumina miseq\"[Properties]"
-                            #      "))",
-                            retmax="3000000")
-    record = Entrez.read(handle)
-
-    identifiers = set()
-    for index, identifier in enumerate(record['IdList']):
-        folder = make_folder(identifier)
-        path = folder + "/" + identifier + ".xml"
-        if os.path.exists(path):
-            continue
-        if not os.path.exists(folder):
-            os.makedirs(folder)
-        identifiers.add(int(identifier))
-
-    num_cores = 2
-    print("Parsing", len(identifiers))
-    try:
-        results = Parallel(n_jobs=num_cores)(delayed(processInput)(i) for i in identifiers)
-        # Stop when finished
-        sys.exit(0)
-    except Exception as e:
-        pass