--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vsnp_determine_ref_from_data.py	Tue Apr 21 10:08:28 2020 -0400
@@ -0,0 +1,367 @@
+#!/usr/bin/env python
+
+import argparse
+import gzip
+import multiprocessing
+import os
+import queue
+import yaml
+from Bio.SeqIO.QualityIO import FastqGeneralIterator
+from collections import OrderedDict
+
+INPUT_READS_DIR = 'input_reads'
+OUTPUT_DBKEY_DIR = 'output_dbkey'
+OUTPUT_METRICS_DIR = 'output_metrics'
+
+
+def get_base_file_name(file_path):
+    base_file_name = os.path.basename(file_path)
+    if base_file_name.find(".") > 0:
+        # Eliminate the extension.
+        return os.path.splitext(base_file_name)[0]
+    elif base_file_name.find("_") > 0:
+        # The dot extension was likely changed to
+        # the " character.
+        items = base_file_name.split("_")
+        no_ext = "_".join(items[0:-2])
+        if len(no_ext) > 0:
+            return no_ext
+    return base_file_name
+
+
+def get_dbkey(dnaprints_dict, key, s):
+    # dnaprints_dict looks something like this:
+    # {'brucella': {'NC_002945v4': ['11001110', '11011110', '11001100']}
+    # {'bovis': {'NC_006895': ['11111110', '00010010', '01111011']}}
+    d = dnaprints_dict.get(key, {})
+    for data_table_value, v_list in d.items():
+        if s in v_list:
+            return data_table_value
+    return ""
+
+
+def get_dnaprints_dict(dnaprint_fields):
+    # A dndprint_fields entry looks something liek this.
+    # [['AF2122', '/galaxy/tool-data/vsnp/AF2122/dnaprints/NC_002945v4.yml']]
+    dnaprints_dict = {}
+    for item in dnaprint_fields:
+        # Here item is a 2-element list of data
+        # table components, # value and path.
+        value = item[0]
+        path = item[1].strip()
+        with open(path, "rt") as fh:
+            # The format of all dnaprints yaml
+            # files is something like this:
+            # brucella:
+            #  - 0111111111111111
+            print_dict = yaml.load(fh, Loader=yaml.Loader)
+        for print_dict_k, print_dict_v in print_dict.items():
+            dnaprints_v_dict = dnaprints_dict.get(print_dict_k, {})
+            if len(dnaprints_v_dict) > 0:
+                # dnaprints_dict already contains k (e.g., 'brucella',
+                # and dnaprints_v_dict will be a dictionary # that
+                # looks something like this:
+                # {'NC_002945v4': ['11001110', '11011110', '11001100']}
+                value_list = dnaprints_v_dict.get(value, [])
+                value_list = value_list + print_dict_v
+                dnaprints_v_dict[value] = value_list
+            else:
+                # dnaprints_v_dict is an empty dictionary.
+                dnaprints_v_dict[value] = print_dict_v
+            dnaprints_dict[print_dict_k] = dnaprints_v_dict
+    # dnaprints_dict looks something like this:
+    # {'brucella': {'NC_002945v4': ['11001110', '11011110', '11001100']}
+    # {'bovis': {'NC_006895': ['11111110', '00010010', '01111011']}}
+    return dnaprints_dict
+
+
+def get_group_and_dbkey(dnaprints_dict, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum):
+    if brucella_sum > 3:
+        group = "Brucella"
+        dbkey = get_dbkey(dnaprints_dict, "brucella", brucella_string)
+    elif bovis_sum > 3:
+        group = "TB"
+        dbkey = get_dbkey(dnaprints_dict, "bovis", bovis_string)
+    elif para_sum >= 1:
+        group = "paraTB"
+        dbkey = get_dbkey(dnaprints_dict, "para", para_string)
+    else:
+        group = ""
+        dbkey = ""
+    return group, dbkey
+
+
+def get_group_and_dbkey_for_collection(task_queue, finished_queue, dnaprints_dict, timeout):
+    while True:
+        try:
+            tup = task_queue.get(block=True, timeout=timeout)
+        except queue.Empty:
+            break
+        fastq_file, count_list, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum = tup
+        group, dbkey = get_group_and_dbkey(dnaprints_dict, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum)
+        finished_queue.put((fastq_file, count_list, group, dbkey))
+        task_queue.task_done()
+
+
+def get_oligo_dict():
+    oligo_dict = {}
+    oligo_dict["01_ab1"] = "AATTGTCGGATAGCCTGGCGATAACGACGC"
+    oligo_dict["02_ab3"] = "CACACGCGGGCCGGAACTGCCGCAAATGAC"
+    oligo_dict["03_ab5"] = "GCTGAAGCGGCAGACCGGCAGAACGAATAT"
+    oligo_dict["04_mel"] = "TGTCGCGCGTCAAGCGGCGTGAAATCTCTG"
+    oligo_dict["05_suis1"] = "TGCGTTGCCGTGAAGCTTAATTCGGCTGAT"
+    oligo_dict["06_suis2"] = "GGCAATCATGCGCAGGGCTTTGCATTCGTC"
+    oligo_dict["07_suis3"] = "CAAGGCAGATGCACATAATCCGGCGACCCG"
+    oligo_dict["08_ceti1"] = "GTGAATATAGGGTGAATTGATCTTCAGCCG"
+    oligo_dict["09_ceti2"] = "TTACAAGCAGGCCTATGAGCGCGGCGTGAA"
+    oligo_dict["10_canis4"] = "CTGCTACATAAAGCACCCGGCGACCGAGTT"
+    oligo_dict["11_canis"] = "ATCGTTTTGCGGCATATCGCTGACCACAGC"
+    oligo_dict["12_ovis"] = "CACTCAATCTTCTCTACGGGCGTGGTATCC"
+    oligo_dict["13_ether2"] = "CGAAATCGTGGTGAAGGACGGGACCGAACC"
+    oligo_dict["14_63B1"] = "CCTGTTTAAAAGAATCGTCGGAACCGCTCT"
+    oligo_dict["15_16M0"] = "TCCCGCCGCCATGCCGCCGAAAGTCGCCGT"
+    oligo_dict["16_mel1b"] = "TCTGTCCAAACCCCGTGACCGAACAATAGA"
+    oligo_dict["17_tb157"] = "CTCTTCGTATACCGTTCCGTCGTCACCATGGTCCT"
+    oligo_dict["18_tb7"] = "TCACGCAGCCAACGATATTCGTGTACCGCGACGGT"
+    oligo_dict["19_tbbov"] = "CTGGGCGACCCGGCCGACCTGCACACCGCGCATCA"
+    oligo_dict["20_tb5"] = "CCGTGGTGGCGTATCGGGCCCCTGGATCGCGCCCT"
+    oligo_dict["21_tb2"] = "ATGTCTGCGTAAAGAAGTTCCATGTCCGGGAAGTA"
+    oligo_dict["22_tb3"] = "GAAGACCTTGATGCCGATCTGGGTGTCGATCTTGA"
+    oligo_dict["23_tb4"] = "CGGTGTTGAAGGGTCCCCCGTTCCAGAAGCCGGTG"
+    oligo_dict["24_tb6"] = "ACGGTGATTCGGGTGGTCGACACCGATGGTTCAGA"
+    oligo_dict["25_para"] = "CCTTTCTTGAAGGGTGTTCG"
+    oligo_dict["26_para_sheep"] = "CGTGGTGGCGACGGCGGCGGGCCTGTCTAT"
+    oligo_dict["27_para_cattle"] = "TCTCCTCGGTCGGTGATTCGGGGGCGCGGT"
+    return oligo_dict
+
+
+def get_seq_counts(value, fastq_list, gzipped):
+    count = 0
+    for fastq_file in fastq_list:
+        if gzipped == "true":
+            with gzip.open(fastq_file, 'rt') as fh:
+                for title, seq, qual in FastqGeneralIterator(fh):
+                    count += seq.count(value)
+        else:
+            with open(fastq_file, 'r') as fh:
+                for title, seq, qual in FastqGeneralIterator(fh):
+                    count += seq.count(value)
+    return(value, count)
+
+
+def get_species_counts(fastq_list, gzipped):
+    count_summary = {}
+    oligo_dict = get_oligo_dict()
+    for v1 in oligo_dict.values():
+        returned_value, count = get_seq_counts(v1, fastq_list, gzipped)
+        for key, v2 in oligo_dict.items():
+            if returned_value == v2:
+                count_summary.update({key: count})
+    count_list = []
+    for v in count_summary.values():
+        count_list.append(v)
+    brucella_sum = sum(count_list[:16])
+    bovis_sum = sum(count_list[16:24])
+    para_sum = sum(count_list[24:])
+    return count_summary, count_list, brucella_sum, bovis_sum, para_sum
+
+
+def get_species_counts_for_collection(task_queue, finished_queue, gzipped, timeout):
+    while True:
+        try:
+            fastq_file = task_queue.get(block=True, timeout=timeout)
+        except queue.Empty:
+            break
+        count_summary, count_list, brucella_sum, bovis_sum, para_sum = get_species_counts([fastq_file], gzipped)
+        finished_queue.put((fastq_file, count_summary, count_list, brucella_sum, bovis_sum, para_sum))
+        task_queue.task_done()
+
+
+def get_species_strings(count_summary):
+    binary_dictionary = {}
+    for k, v in count_summary.items():
+        if v > 1:
+            binary_dictionary.update({k: 1})
+        else:
+            binary_dictionary.update({k: 0})
+    binary_dictionary = OrderedDict(sorted(binary_dictionary.items()))
+    binary_list = []
+    for v in binary_dictionary.values():
+        binary_list.append(v)
+    brucella_binary = binary_list[:16]
+    brucella_string = ''.join(str(e) for e in brucella_binary)
+    bovis_binary = binary_list[16:24]
+    bovis_string = ''.join(str(e) for e in bovis_binary)
+    para_binary = binary_list[24:]
+    para_string = ''.join(str(e) for e in para_binary)
+    return brucella_string, bovis_string, para_string
+
+
+def get_species_strings_for_collection(task_queue, finished_queue, timeout):
+    while True:
+        try:
+            tup = task_queue.get(block=True, timeout=timeout)
+        except queue.Empty:
+            break
+        fastq_file, count_summary, count_list, brucella_sum, bovis_sum, para_sum = tup
+        brucella_string, bovis_string, para_string = get_species_strings(count_summary)
+        finished_queue.put((fastq_file, count_list, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum))
+        task_queue.task_done()
+
+
+def output_dbkey(file_name, dbkey, output_file=None):
+    # Output the dbkey.
+    if output_file is None:
+        # We're producing a dataset collection.
+        output_file = os.path.join(OUTPUT_DBKEY_DIR, "%s.txt" % file_name)
+    with open(output_file, "w") as fh:
+        fh.write("%s" % dbkey)
+
+
+def output_files(fastq_file, count_list, group, dbkey, dbkey_file=None, metrics_file=None):
+    base_file_name = get_base_file_name(fastq_file)
+    if dbkey_file is not None:
+        # We're dealing with a single read or
+        # a set of paired reads.  If the latter,
+        # the following will hopefully produce a
+        # good sample string.
+        if base_file_name.find("_") > 0:
+            base_file_name = base_file_name.split("_")[0]
+    output_dbkey(base_file_name, dbkey, dbkey_file)
+    output_metrics(base_file_name, count_list, group, dbkey, metrics_file)
+
+
+def output_files_for_collection(task_queue, timeout):
+    while True:
+        try:
+            tup = task_queue.get(block=True, timeout=timeout)
+        except queue.Empty:
+            break
+        fastq_file, count_list, group, dbkey = tup
+        output_files(fastq_file, count_list, group, dbkey)
+        task_queue.task_done()
+
+
+def output_metrics(file_name, count_list, group, dbkey, output_file=None):
+    # Output the metrics.
+    if output_file is None:
+        # We're producing a dataset collection.
+        output_file = os.path.join(OUTPUT_METRICS_DIR, "%s.txt" % file_name)
+    with open(output_file, "w") as fh:
+        fh.write("Sample: %s\n" % file_name)
+        fh.write("Brucella counts: ")
+        for i in count_list[:16]:
+            fh.write("%d," % i)
+        fh.write("\nTB counts: ")
+        for i in count_list[16:24]:
+            fh.write("%d," % i)
+        fh.write("\nPara counts: ")
+        for i in count_list[24:]:
+            fh.write("%d," % i)
+        fh.write("\nGroup: %s" % group)
+        fh.write("\ndbkey: %s\n" % dbkey)
+
+
+def set_num_cpus(num_files, processes):
+    num_cpus = int(multiprocessing.cpu_count())
+    if num_files < num_cpus and num_files < processes:
+        return num_files
+    if num_cpus < processes:
+        half_cpus = int(num_cpus / 2)
+        if num_files < half_cpus:
+            return num_files
+        return half_cpus
+    return processes
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, help="List of dnaprints data table value, name and path fields")
+    parser.add_argument('--read1', action='store', dest='read1', required=False, default=None, help='Required: single read')
+    parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
+    parser.add_argument('--gzipped', action='store', dest='gzipped', help='Input files are gzipped')
+    parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', required=False, default=None, help='Output reference file')
+    parser.add_argument('--output_metrics', action='store', dest='output_metrics', required=False, default=None, help='Output metrics file')
+    parser.add_argument('--processes', action='store', dest='processes', type=int, help='User-selected number of processes to use for job splitting')
+
+    args = parser.parse_args()
+
+    collection = False
+    fastq_list = []
+    if args.read1 is not None:
+        fastq_list.append(args.read1)
+        if args.read2 is not None:
+            fastq_list.append(args.read2)
+    else:
+        collection = True
+        for file_name in sorted(os.listdir(INPUT_READS_DIR)):
+            file_path = os.path.abspath(os.path.join(INPUT_READS_DIR, file_name))
+            fastq_list.append(file_path)
+
+    # The value of dnaprint_fields is a list of lists, where each list is
+    # the [value, name, path] components of the vsnp_dnaprints data table.
+    # The data_manager_vsnp_dnaprints tool assigns the dbkey column from the
+    # all_fasta data table to the value column in the vsnp_dnaprints data
+    # table to ensure a proper mapping for discovering the dbkey.
+    dnaprints_dict = get_dnaprints_dict(args.dnaprint_fields)
+
+    if collection:
+        # Here fastq_list consists of any number of
+        # reads, so each file will be processed and
+        # dataset collections will be produced as outputs.
+        multiprocessing.set_start_method('spawn')
+        queue1 = multiprocessing.JoinableQueue()
+        queue2 = multiprocessing.JoinableQueue()
+        num_files = len(fastq_list)
+        cpus = set_num_cpus(num_files, args.processes)
+        # Set a timeout for get()s in the queue.
+        timeout = 0.05
+
+        for fastq_file in fastq_list:
+            queue1.put(fastq_file)
+
+        # Complete the get_species_counts task.
+        processes = [multiprocessing.Process(target=get_species_counts_for_collection, args=(queue1, queue2, args.gzipped, timeout, )) for _ in range(cpus)]
+        for p in processes:
+            p.start()
+        for p in processes:
+            p.join()
+        queue1.join()
+
+        # Complete the get_species_strings task.
+        processes = [multiprocessing.Process(target=get_species_strings_for_collection, args=(queue2, queue1, timeout, )) for _ in range(cpus)]
+        for p in processes:
+            p.start()
+        for p in processes:
+            p.join()
+        queue2.join()
+
+        # Complete the get_group_and_dbkey task.
+        processes = [multiprocessing.Process(target=get_group_and_dbkey_for_collection, args=(queue1, queue2, dnaprints_dict, timeout, )) for _ in range(cpus)]
+        for p in processes:
+            p.start()
+        for p in processes:
+            p.join()
+        queue1.join()
+
+        # Complete the output_files task.
+        processes = [multiprocessing.Process(target=output_files_for_collection, args=(queue2, timeout, )) for _ in range(cpus)]
+        for p in processes:
+            p.start()
+        for p in processes:
+            p.join()
+        queue2.join()
+
+        if queue1.empty() and queue2.empty():
+            queue1.close()
+            queue1.join_thread()
+            queue2.close()
+            queue2.join_thread()
+    else:
+        # Here fastq_list consists of either a single read
+        # or a set of paired reads, producing single outputs.
+        count_summary, count_list, brucella_sum, bovis_sum, para_sum = get_species_counts(fastq_list, args.gzipped)
+        brucella_string, bovis_string, para_string = get_species_strings(count_summary)
+        group, dbkey = get_group_and_dbkey(dnaprints_dict, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum)
+        output_files(args.read1, count_list, group, dbkey, dbkey_file=args.output_dbkey, metrics_file=args.output_metrics)