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- ALO headers in cluster_metrics and cafe are in wrong order
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,230 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
|
|
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| """ | ||
| usage: find_isoforms.py -i <FILE> [-o <STRING>] | ||
| [-h|--help] | ||
| Options: | ||
| -h --help show this | ||
| -i, --infile <FILE> Infile | ||
| -o, --outprefix <STRING> Output prefix | ||
| """ | ||
|
|
||
| import re | ||
| import sys | ||
| import operator | ||
| from docopt import docopt | ||
| from os.path import isfile, join, exists, realpath, dirname, basename | ||
|
|
||
| def parse_groups(group_f): | ||
| with open(groups_f) as group_fh: | ||
| for line in group_fh: | ||
| clusterID, protein_string = line.rstrip("\n").split(": ") | ||
| proteins = protein_string.split(" ") | ||
| if headers: | ||
| for protein in proteins: | ||
| if protein in headers: | ||
| if headers[protein] == None: | ||
| headers[protein] = clusterID | ||
| output[clusterID] = proteins | ||
| else: | ||
| sys.exit("[-] protein %s found more than once" % protein) | ||
| else: | ||
| if clusterID in clusters: | ||
| if clusters[clusterID] == None: | ||
| clusters[clusterID] = clusterID | ||
| output[clusterID] = proteins | ||
| else: | ||
| sys.exit("[-] cluster %s found more than once" % clusterID) | ||
| return output | ||
|
|
||
| def read_file(infile): | ||
| if not infile or not exists(infile): | ||
| sys.exit("[ERROR] - File '%s' does not exist." % (infile)) | ||
| if infile.endswith(".gz"): | ||
| import gzip | ||
| with gzip.open(infile) as fh: | ||
| for line in fh: | ||
| yield line.rstrip("\n") | ||
| else: | ||
| with open(infile) as fh: | ||
| for line in fh: | ||
| yield line.rstrip("\n") | ||
|
|
||
| class BarChartObj(): | ||
| def __init__(self, IV): | ||
| self.IV = IV | ||
| self.proteins_conserved = {'non-singletons-split' : set(), 'non-singletons' : set(), 'singletons' : set()} | ||
| self.proteins_non_conserved = {'non-singletons-split' : set(), 'non-singletons' : set(), 'singletons' : set()} | ||
| self.proteins_singletons = {'non-singletons-split' : set(), 'non-singletons' : set(), 'singletons' : set()} | ||
|
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|
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| class DataCollection(): | ||
| def __init__(self): | ||
| self.clusterCollections = [] | ||
| self.protein_ids_by_hierarchality_pattern = {} # tuples of hierarchality | ||
| self.hierarchality_pattern_by_protein_id = {} | ||
| self.hierarchality_pattern_by_protein_ids = {} | ||
| self.protein_ids_trajectory = {} | ||
| self.cluster_ids_trajectory = {} | ||
|
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|
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| def add_to_hierarchy(self, protein_ids_hierarchy, protein_ids): | ||
| if protein_ids_hierarchy[protein_ids]: | ||
| protein_ids_hierarchy[protein_ids] | ||
|
|
||
| def add_clusterCollection(self, clusterCollection): | ||
| barChartObj = BarChartObj(clusterCollection.IV) | ||
|
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||
| cluster_counts_by_split = {'conserved': {'singleton': 0, 'non_singleton' : 0}, 'hierarchical' : {'singleton': 0, 'non_singleton' : 0}, 'non_hierarchical' : 0} | ||
| protein_counts_by_split = {'conserved': {'singleton': 0, 'non_singleton' : 0}, 'hierarchical' : {'singleton': 0, 'non_singleton' : 0}, 'non_hierarchical' : 0} | ||
| cluster_ids_by_split = {'conserved': {'singleton': set(), 'non_singleton' : set()}, 'hierarchical' : {'singleton': set(), 'non_singleton' : set()}, 'non_hierarchical' : set()} | ||
| protein_ids_by_split = {'conserved': {'singleton': set(), 'non_singleton' : set()}, 'hierarchical' : {'singleton': set(), 'non_singleton' : set()}, 'non_hierarchical' : set()} | ||
| if self.clusterCollections == []: | ||
| self.clusterCollections.append(clusterCollection) | ||
| cluster_counts_by_split['conserved']['singleton'] += clusterCollection.cluster_singleton_count | ||
| cluster_counts_by_split['conserved']['non_singleton'] += clusterCollection.cluster_non_singleton_count | ||
| protein_counts_by_split['conserved']['singleton'] += clusterCollection.protein_singleton_count | ||
| protein_counts_by_split['conserved']['non_singleton'] += clusterCollection.protein_count | ||
| else: | ||
| parent_clusterCollection = self.clusterCollections[-1] | ||
| child_clusterCollection = child_clusterCollection | ||
| non_hierarchical_cluster_ids = set() | ||
|
|
||
| for parent_protein_ids, prev_cluster_id in parent_clusterCollection.cluster_id_by_protein_ids.items(): | ||
| # for each previous cluster | ||
| if parent_protein_ids in child_clusterCollection.cluster_id_by_protein_ids: | ||
| # if cluster is present in current clustering => conserved, no-split | ||
| split = 'None' | ||
| else: | ||
| # cluster is split somehow: hierarchical (singleton/non-singleton), non-hierarchical (non-singleton) | ||
| protein_ids_split_in_singleton = [] | ||
| protein_ids_split_in_non_singleton = [] | ||
| for parent_protein_id in parent_protein_ids: | ||
| # for each protein in previous cluster | ||
| if parent_protein_id in child_clusterCollection.cluster_id_by_protein_ids: | ||
| # if singleton | ||
| protein_ids_split_in_singleton.append(parent_protein_id) | ||
| else: | ||
| # not a singleton | ||
| protein_ids_split_in_non_singleton.append(parent_protein_id) | ||
| if protein_ids_split_in_non_singleton: | ||
| non_singleton_clusters = set() | ||
| for protein_id in protein_ids_split_in_non_singleton: | ||
| non_singleton_clusters.add(clusterCollection.cluster_id_by_protein_id[protein_id]) | ||
| for non_singleton_cluster in non_singleton_clusters: | ||
| # check if additional proteins are present | ||
| protein_ids_in_non_singleton_cluster = clusterCollection.clusterObjs_by_cluster_id[non_singleton_cluster] | ||
| additional_protein_ids = protein_ids_in_non_singleton_cluster.difference(parent_protein_ids) | ||
| if additional_protein_ids: | ||
| if not non_singleton_cluster in non_hierarchical_cluster_ids: | ||
| non_hierarchical_cluster_count += 1 | ||
| non_hierarchical_cluster_ids.add(non_singleton_cluster) | ||
| non_hierarchical_split_count += 1 | ||
| else: | ||
| hierarchical_cluster_count += 1 | ||
| hierarchical_split_count += 1 | ||
|
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| "non-hierarchical" | ||
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| else: | ||
| if len(protein_ids) == 1: | ||
| hierarchality = "split_singleton" | ||
| else: | ||
| hierarchality = "split_non_singleton" | ||
| for protein_id in protein_ids: | ||
| if not protein_id in self.hierarchality_pattern_by_protein_id: | ||
| self.hierarchality_pattern_by_protein_id[protein_id] = [] | ||
| self.hierarchality_pattern_by_protein_id[protein_id].append(hierarchality) | ||
| if not protein_ids in self.hierarchality_pattern_by_protein_ids: | ||
| self.hierarchality_pattern_by_protein_ids[protein_ids] = [] | ||
| self.hierarchality_pattern_by_protein_ids[protein_ids].append(hierarchality) | ||
| self.clusterCollections.append(clusterCollection) | ||
|
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||
| def generate_output(self): | ||
| for protein_ids, hierarchality_patterns in self.hierarchality_pattern_by_protein_ids.items(): | ||
| print "proteins: %s" % (len(protein_ids)), hierarchality_patterns | ||
|
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||
| class ClusterObj(): | ||
| def __init__(self, IV, cluster_id, protein_ids): | ||
| self.IV = IV | ||
| self.cluster_id = cluster_id | ||
| self.protein_ids = protein_ids | ||
| self.protein_count = len(protein_ids) | ||
| self.singleton = True if len(protein_ids) == 1 else False | ||
| self.validated = False | ||
|
|
||
| class ClusterCollection(): | ||
| def __init__(self, IV, cluster_f): | ||
| self.IV = IV | ||
| self.cluster_f = cluster_f | ||
|
|
||
| self.cluster_id_by_protein_id = {} | ||
| self.cluster_id_by_protein_ids = {} | ||
| self.clusterObjs_by_cluster_id = {} | ||
|
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| self.cluster_ids_by_cluster_status = {} | ||
|
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| self.cluster_count = 0 | ||
| self.protein_count = 0 | ||
| self.cluster_singleton_count = 0 | ||
| self.protein_singleton_count = 0 | ||
| self.cluster_non_singleton_count = 0 | ||
| self.protein_non_singleton_count = 0 | ||
|
|
||
| def parse_cluster_f(self): | ||
| print "[+] Parsing cluster file %s ..." % (self.cluster_f) | ||
| for line in read_file(self.cluster_f): | ||
| cluster_id_string, protein_string = line.rstrip("\n").split(": ") | ||
| cluster_id = "%s:%s" % (self.IV, cluster_id_string) | ||
| protein_ids = protein_string.split(" ") | ||
| clusterObj = ClusterObj(self.IV, cluster_id, protein_ids) | ||
| # count | ||
| if clusterObj.singleton == True: | ||
| self.cluster_singleton_count += 1 | ||
| self.protein_singleton_count += len(clusterObj.protein_count) | ||
| else: | ||
| self.cluster_non_singleton_count += 1 | ||
| self.protein_non_singleton_count += len(clusterObj.protein_count) | ||
| self.cluster_count += 1 | ||
| self.protein_count += len(clusterObj.protein_count) | ||
| # add | ||
| for protein_id in clusterObj.protein_ids: | ||
| self.cluster_id_by_protein_id[protein_id] = clusterObj.cluster_id | ||
| self.cluster_id_by_protein_ids[frozenset(clusterObj.protein_ids)] = clusterObj.cluster_id | ||
| self.clusterObjs_by_cluster_id[clusterObj.cluster_id] = clusterObj | ||
|
|
||
| class InputObj(): | ||
| def __init__(self, input_f): | ||
| self.input_file_by_IV = self.parse_input_f(input_f) | ||
|
|
||
| def parse_input_f(self, input_f): | ||
| print "[+] Parsing input file %s ..." % (input_f) | ||
| input_file_by_IV = {} | ||
| for line in read_file(input_f): | ||
| temp = line.split() | ||
| IV = temp[0] | ||
| cluster_f = temp[1] | ||
| input_file_by_IV[IV] = cluster_f | ||
| return input_file_by_IV | ||
|
|
||
| if __name__ == "__main__": | ||
| __version__ = 0.1 | ||
| args = docopt(__doc__) | ||
|
|
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| input_f = args['--infile'] | ||
| out_prefix = args['--outprefix'] | ||
|
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| inputObj = InputObj(input_f) | ||
| print "[+] Start ..." | ||
| dataCollection = DataCollection() | ||
| for IV, cluster_f in sorted(inputObj.input_file_by_IV.items()): | ||
| clusterCollection = ClusterCollection(IV, cluster_f) | ||
| clusterCollection.parse_cluster_f() | ||
| dataCollection.add_clusterCollection(clusterCollection) | ||
| dataCollection.generate_output() |
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