PyamilySeq 0.9.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

PyamilySeq/PyamilySeq_Species.py

@@ -1,287 +0,0 @@
-#from line_profiler_pycharm import profile
-
-import math
-
-try:
-    from .Constants import *
-    from .clusterings import *
-    from .utils import *
-except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
-    from Constants import *
-    from clusterings import *
-    from utils import *
-
-
-#def output_fasta(options, gene_families):
-
-def gene_presence_absence_output(options, genome_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted):
-    print("Outputting gene_presence_absence file")
-    output_dir = os.path.abspath(options.output_dir)
-    in_name = options.clusters.split('.')[0].split('/')[-1]
-    gpa_outfile = os.path.join(output_dir, in_name)
-    gpa_outfile = open(gpa_outfile+'_gene_presence_absence.csv','w')
-    gpa_outfile.write('"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences","Avg sequences per isolate","Genome Fragment","Order within Fragment","'
-                     '"Accessory Fragment","Accessory Order with Fragment","QC","Min group size nuc","Max group size nuc","Avg group size nuc","')
-    gpa_outfile.write('","'.join(genome_dict.keys()))
-    gpa_outfile.write('"\n')
-    for cluster, sequences in pangenome_clusters_First_sequences_sorted.items():
-        average_sequences_per_genome = len(sequences) / len(pangenome_clusters_First_sorted[cluster])
-        gpa_outfile.write('"group_'+str(cluster)+'","","'+str(len(pangenome_clusters_First_sorted[cluster]))+'","'+str(len(sequences))+'","'+str(average_sequences_per_genome)+
-                         '","","","","","","","","",""')
-
-
-        for genome in genome_dict.keys():
-            full_out = ''
-            tmp_list = []
-            for value in sequences:
-                if value.split('|')[0] == genome:
-                    tmp_list.append(value)
-            if tmp_list:
-                full_out += ',"'+''.join(tmp_list)+'"'
-            else:
-                full_out = ',""'
-            gpa_outfile.write(full_out)
-        gpa_outfile.write('\n')
-
-### Below is some unfinished code
-    # edge_list_outfile = open(in_name+'_edge_list.csv','w')
-    # for cluster, sequences in pangenome_clusters_First_sequences_sorted.items():
-    #     output = []
-    #     for entry in sequences:
-    #         # Split each entry at '|'
-    #         genome, gene = entry.split('|')
-    #         # Format the result as "gene  genome"
-    #         output.append(f"{gene}\t{genome}")
-    #     for line in output:
-    #         edge_list_outfile.write(line + '\n')
-
-
-
-
-def get_cores(options,genome_dict):
-    ##Calculate core groups
-    groups = OrderedDict()
-    cores = OrderedDict()
-    prev_top = len(genome_dict)
-    first = True
-    for group in options.core_groups.split(','):
-        calculated_floor = math.floor(int(group) / 100 * len(genome_dict))
-        if first == False:
-            groups[group] = (calculated_floor,prev_top)
-        else:
-            groups[group] = (calculated_floor, prev_top)
-            first = False
-        prev_top = calculated_floor
-        first_core_group = 'First_core_' + group
-        cores[first_core_group] = []
-        if options.reclustered != None:
-            extended_core_group = 'extended_core_' + group
-            cores[extended_core_group] = []
-            combined_core_group = 'combined_core_' + group
-            cores[combined_core_group] = []
-            second_core_group = 'Second_core_' + group
-            cores[second_core_group] = []
-            only_second_core_group = 'only_Second_core_' + group
-            cores[only_second_core_group] = []
-    return cores, groups
-
-#@profile
-def calc_First_only_core(cluster, First_num, groups, cores):
-    groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= int(First_num) <= fir):
-        res = idx
-    family_group = list(groups)[res]
-    cores['First_core_'+family_group].append(cluster)
-
-#@profile
-def calc_single_First_extended_Second_only_core(cluster, First_num, groups, cores, Second_num): # Count gene families extended with StORFs
-    groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= First_num+Second_num <= fir):
-        res = idx
-
-    family_group = list(groups)[res]
-    cores['extended_core_' + family_group].append(cluster)
-
-
-#@profile
-def calc_multi_First_extended_Second_only_core(cluster, First_num, groups, cores, Second_num): # Count seperately those gene families extended with StORF_Reporter but combined >1 PEP
-    groups_as_list = list(groups.values())
-    # Looping through the list to find the matching condition
-    for idx, (sec, fir) in enumerate(groups_as_list):
-        if sec <= First_num + Second_num <= fir:
-            res = idx
-            break
-    family_group = list(groups)[res]
-    cores['combined_core_' + family_group].append(cluster)
-
-
-#@profile
-def calc_Second_only_core(cluster, Second_num, groups, cores):
-    groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= Second_num <= fir):
-        res = idx
-    family_group = list(groups)[res]
-    cores['Second_core_' + family_group].append(cluster)
-
-#@profile
-def calc_only_Second_only_core(cluster, Second_num, groups, cores): # only count the true storf onlies
-    groups_as_list = list(groups.values())
-    for idx in (idx for idx, (sec, fir) in enumerate(groups_as_list) if sec <= Second_num <= fir):
-        res = idx
-    family_group = list(groups)[res]
-    cores['only_Second_core_' + family_group].append(cluster)
-
-
-
-#@profile
-def cluster(options):
-
-    if options.cluster_format == 'CD-HIT':
-        genome_dict, pangenome_clusters_First, pangenome_clusters_First_genomes, pangenome_clusters_First_sequences, reps = cluster_CDHIT(options, '|')
-    elif 'TSV' in options.cluster_format or 'CSV' in options.cluster_format:
-        genome_dict, pangenome_clusters_First, pangenome_clusters_First_genomes, pangenome_clusters_First_sequences, reps = cluster_EdgeList(options, '|')
-
-    ###
-    cores, groups = get_cores(options, genome_dict)
-    ###
-
-    if options.reclustered != None:
-        if options.cluster_format == 'CD-HIT':
-            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second, combined_pangenome_clusters_Second_sequences = combined_clustering_CDHIT(options, genome_dict, '|')
-        elif 'TSV' in options.cluster_format or 'CSV' in options.cluster_format:
-            #Fix
-            combined_pangenome_clusters_First_Second_clustered,not_Second_only_cluster_ids,combined_pangenome_clusters_Second,combined_pangenome_clusters_Second_sequences  = combined_clustering_Edge_List(options, '|')
-        pangenome_clusters_Type = combined_clustering_counting(options, pangenome_clusters_First, reps, combined_pangenome_clusters_First_Second_clustered, pangenome_clusters_First_genomes, '|')
-    else:
-        pangenome_clusters_Type = single_clustering_counting(pangenome_clusters_First, reps)
-
-
-
-    Number_Of_Second_Extending_But_Same_Genomes = 0
-
-    sorted_first_keys = sort_keys_by_values(pangenome_clusters_First, pangenome_clusters_First_sequences)
-    pangenome_clusters_First_sorted = reorder_dict_by_keys(pangenome_clusters_First, sorted_first_keys)
-    pangenome_clusters_First_sequences_sorted = reorder_dict_by_keys(pangenome_clusters_First_sequences, sorted_first_keys)
-    pangenome_clusters_Type_sorted = reorder_dict_by_keys(pangenome_clusters_Type, sorted_first_keys)
-
-    print("Calculating Groups")
-    seen_groupings = []
-    for cluster, numbers in pangenome_clusters_Type_sorted.items():
-    ############################### Calculate First only
-        cluster = str(cluster)
-        if '78' in cluster:
-            pass
-        for grouping in numbers[2]: #!!# Could do with a more elegant solution
-            current_cluster = grouping[0].split(':')[0]
-            if current_cluster not in seen_groupings:
-                seen_groupings.append(current_cluster)
-                current_cluster_size = grouping[0].split(':')[1]
-                calc_First_only_core(current_cluster, current_cluster_size,groups,cores)
-            ############################# Calculate First and Reclustered-Second
-                if numbers[0] == 1 and numbers[3] >= 1:  # If Seconds did not combine First reps
-                    calc_single_First_extended_Second_only_core(cluster, numbers[1], groups, cores, numbers[3])
-                elif numbers[0] > 1 and numbers[3] >= 1:  # If unique Seconds combined multiple Firsts
-                    calc_multi_First_extended_Second_only_core(cluster, numbers[1], groups, cores, numbers[3])
-                elif numbers[4] >= 1:
-                    Number_Of_Second_Extending_But_Same_Genomes += 1
-            else:
-                if options.verbose == True:
-                    print("First cluster " + current_cluster + " already processed - This is likely because it was clustered with another First representative.")
-
-    if options.reclustered != None:
-        combined_pangenome_clusters_ONLY_Second_Type = defaultdict(list)
-        combined_pangenome_clusters_Second_Type = defaultdict(list)
-        for cluster, genomes in combined_pangenome_clusters_Second.items():
-            if cluster in not_Second_only_cluster_ids:
-                combined_pangenome_clusters_Second_Type[cluster] = [cluster, len(genomes)]
-            else:
-                combined_pangenome_clusters_ONLY_Second_Type[cluster] = [cluster, len(genomes)]
-        for cluster, data in combined_pangenome_clusters_Second_Type.items():
-            if data[1] >= 1:
-                calc_Second_only_core(cluster, data[1], groups, cores)
-        for cluster, data in combined_pangenome_clusters_ONLY_Second_Type.items():
-            if data[1] >= 1:
-                calc_only_Second_only_core(cluster, data[1], groups, cores)
-    ###########################
-    ### Output
-    output_path = os.path.abspath(options.output_dir)
-    if not os.path.exists(output_path):
-        os.makedirs(output_path)
-    stats_out = os.path.join(output_path,'summary_statistics.txt')
-    key_order = ['First_core_', 'extended_core_', 'combined_core_', 'Second_core_','only_Second_core_']
-    with open(stats_out, 'w') as outfile:
-        print("Gene Groups:")
-        outfile.write("Gene Groups:\n")
-        for key_prefix in key_order:
-            for key, value in cores.items():
-                if key.startswith(key_prefix):
-                    print(f"{key}: {len(value)}")
-                    outfile.write(f"{key}: {len(value)}\n")
-        print("Total Number of First Gene Groups (Including Singletons): " + str(len(pangenome_clusters_First_sequences_sorted)))
-        outfile.write("Total Number of First Gene Groups (Including Singletons): " + str(len(pangenome_clusters_First_sequences_sorted)))
-        if options.reclustered!= None:
-            print("Total Number of Second Gene Groups (Including Singletons): " + str(
-                len(combined_pangenome_clusters_Second_sequences)))
-            print("Total Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: " + str(
-                Number_Of_Second_Extending_But_Same_Genomes))
-            outfile.write("\nTotal Number of Second Gene Groups (Including Singletons): " + str(
-                len(combined_pangenome_clusters_Second_sequences)))
-            outfile.write("\nTotal Number of First Gene Groups That Had Additional Second Sequences But Not New Genomes: " + str(
-                Number_Of_Second_Extending_But_Same_Genomes))
-        #Report number of first and second clusters and do the ame for genus
-    if options.gene_presence_absence_out != False:
-        gene_presence_absence_output(options,genome_dict, pangenome_clusters_First_sorted, pangenome_clusters_First_sequences_sorted)
-
-
-    ###Need to fix this below. If full/partial the ifs need to be different. If full we first need to output the gfs then align. if -wruite-groups not presented then it needs
-    # to be done for alignment full anyway...
-
-    if options.run_mode == 'Full':
-        if options.reclustered == None:
-            combined_pangenome_clusters_Second_sequences = None
-        if options.write_groups != None:
-            print("Outputting gene group FASTA files")
-            sequences = read_fasta(options.fasta)
-            #output_dir = os.path.dirname(os.path.abspath(options.output_dir))
-            output_dir = os.path.join(options.output_dir, 'Gene_Families_Output')
-            write_groups(options,output_dir, key_order, cores, sequences,
-                         pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences)
-
-            if options.align_core != None:
-                print("Processing gene group alignment")
-                process_gene_families(options, output_dir, 'concatenated_genes_aligned.fasta')
-
-    elif options.run_mode == 'Partial':
-        if options.reclustered == None:
-            combined_pangenome_clusters_Second_sequences = None
-        if options.write_groups != None and options.fasta != None:
-            print("Outputting gene group FASTA files")
-            sequences = read_fasta(options.fasta)
-            output_dir = os.path.join(options.output_dir, 'Gene_Families_Output')
-            write_groups(options,output_dir, key_order, cores, sequences,
-                         pangenome_clusters_First_sequences_sorted, combined_pangenome_clusters_Second_sequences)
-
-            if options.align_core != None:
-                print("Processing gene group alignment")
-                process_gene_families(options, output_dir, 'concatenated_genes_aligned.fasta')
-
-
-
-        #
-        # if options.align_core != None:
-        #     #output_dir = os.path.dirname(os.path.abspath(options.output_dir))
-        #     output_dir = os.path.join(options.output_dir, 'Gene_Families_Output')
-        #     if not os.path.exists(output_dir):
-        #         os.makedirs(output_dir)
-        #     process_gene_families(options, output_dir, 'concatenated_genes_aligned.fasta')
-
-    #
-    # elif options.run_mode == 'Partial':
-    #     if options.align_core != None and options.fasta != None and options.write_groups != None:
-    #         process_gene_families(options, os.path.join(output_dir, 'Gene_Families_Output'), 'concatenated_genes_aligned.fasta')
-    #
-    #
-    #
-    #
-    #
-

PyamilySeq/Seq_Combiner.py

@@ -1,67 +0,0 @@
-import argparse
-
-
-try:
-    from .Constants import *
-    from .utils import *
-except (ModuleNotFoundError, ImportError, NameError, TypeError) as error:
-    from Constants import *
-    from utils import *
-
-
-
-def main():
-    parser = argparse.ArgumentParser(description='PyamilySeq ' + PyamilySeq_Version + ': Seq-Combiner - A tool to extract sequences from GFF/FASTA files and prepare them for PyamilySeq.')
-    ### Required Arguments
-    required = parser.add_argument_group('Required Arguments')
-    required.add_argument('-input_dir', action='store', dest='input_dir',
-                          help='Directory location where the files are located.',
-                          required=True)
-    required.add_argument('-input_type', action='store', dest='input_type', choices=['separate', 'combined', 'fasta'],
-                          help='Type of input files: "separate" for separate FASTA and GFF files,'
-                             ' "combined" for GFF files with embedded FASTA sequences and "fasta" for combining multiple '
-                               'FASTA files together.',
-                          required=True)
-    required.add_argument("-name_split", action="store", dest="name_split",
-                          help="substring used to split the filename and extract the genome name ('_combined.gff3' or '.gff').",
-                          required=True)
-    required.add_argument("-output_dir", action="store", dest="output_dir",
-                          help="Directory for all output files.",
-                          required=True)
-    required.add_argument("-output_name", action="store", dest="output_file",
-                          help="Output file name.",
-                          required=True)
-
-    optional = parser.add_argument_group('Optional Arguments')
-    optional.add_argument('-gene_ident', action='store', dest='gene_ident', default='CDS',
-                          help='Default - "CDS": Identifier used for extraction of sequences such as "misc_RNA,gene,mRNA,CDS,rRNA,tRNA,tmRNA,CRISPR,ncRNA,regulatory_region,oriC,pseudo"'
-                               ' - Not compatible with "fasta" input mode.',
-                          required=False)
-    optional.add_argument('-translate', action='store_true', dest='translate', default=None,
-                          help='Default - False: Translate extracted sequences to their AA counterpart?',
-                          required=False)
-    misc = parser.add_argument_group('Misc Arguments')
-    misc.add_argument("-v", "--version", action="version",
-                      version=f"PyamilySeq: Seq-Combiner version {PyamilySeq_Version} - Exiting",
-                      help="Print out version number and exit")
-
-    options = parser.parse_args()
-
-    if options.version:
-        sys.exit(PyamilySeq_Version)
-
-    output_path = os.path.abspath(options.output_dir)
-    if not os.path.exists(output_path):
-        os.makedirs(output_path)
-
-    combined_out_file = os.path.join(output_path, options.output_file)
-
-    if options.input_type == 'separate':
-        read_separate_files(options.input_dir, options.name_split, options.gene_ident, combined_out_file, options.translate)
-    elif options.input_type == 'combined':
-        read_combined_files(options.input_dir, options.name_split, options.gene_ident, combined_out_file, options.translate)
-    elif options.input_type == 'fasta':
-        read_fasta_files(options.input_dir, options.name_split, combined_out_file, options.translate)
-
-if __name__ == "__main__":
-    main()