switch to simple id distributor as thread safety is not needed acrros…

… differnt processes

src/common.py

@@ -9,25 +9,13 @@
 import os
 import re
 import subprocess
-import threading
 import math
 from collections import defaultdict
 from enum import Enum
 
 logger = logging.getLogger('IsoQuant')
 
 
-class AtomicIDDistributor(object):
- def __init__(self):
- self.value = 0
- self._lock = threading.Lock()
-
- def increment(self):
- with self._lock:
- self.value += 1
- return self.value
-
-
 class CigarEvent(Enum):
  match = 0
  insertion = 1
@@ -48,6 +36,13 @@ def get_ins_del_match_events(cls):
  return {cls.match, cls.insertion, cls.deletion, cls.seq_match, cls.seq_mismatch}
 
 
+class TranscriptNaming:
+ transcript_prefix = "transcript"
+ novel_gene_prefix = "novel_gene_"
+ nic_transcript_suffix = ".nic"
+ nnic_transcript_suffix = ".nnic"
+
+
 # key, value
 def get_first_best_from_sorted(sorted_list_of_pairs):
  if not sorted_list_of_pairs:

src/gene_info.py

@@ -16,11 +16,10 @@
  equal_ranges,
  get_intron_strand,
  intervals_total_length,
- is_subprofile,
  overlaps,
- junctions_from_blocks,
- AtomicIDDistributor
+ junctions_from_blocks
 )
+from .id_policy import SimpleIDDistributor
 
 logger = logging.getLogger('IsoQuant')
 
@@ -121,7 +120,7 @@ def print_debug(self):
 
 # exon/intron info
 class FeatureInfo:
- feature_id_counter = AtomicIDDistributor()
+ feature_id_counter = SimpleIDDistributor()
  def __init__(self, chr_id, start, end, strand, type, gene_ids):
  self.id = FeatureInfo.feature_id_counter.increment()
  self.chr_id = chr_id

src/graph_based_model_construction.py

@@ -11,6 +11,7 @@
 from enum import unique, Enum
 
 from .common import (
+ TranscriptNaming,
  cmp,
  get_exons,
  intersection_len,
@@ -46,10 +47,6 @@ class StrandnessReportingLevel(Enum):
 
 
 class GraphBasedModelConstructor:
- transcript_prefix = "transcript"
- novel_gene_prefix = "novel_gene_"
- nic_transcript_suffix = ".nic"
- nnic_transcript_suffix = ".nnic"
  detected_known_isoforms = set()
  extended_transcript_ids = set()
 
@@ -411,7 +408,7 @@ def construct_fl_isoforms(self):
  transcript_range = (path[0][1], path[-1][1])
  novel_exons = get_exons(transcript_range, list(intron_path))
  count = self.path_storage.paths[path]
- new_transcript_id = self.transcript_prefix + str(self.get_transcript_id())
+ new_transcript_id = TranscriptNaming.transcript_prefix + str(self.get_transcript_id())
  # logger.debug("uuu %s: %s" % (new_transcript_id, str(novel_exons)))
 
  reference_isoform = None
@@ -482,17 +479,17 @@ def construct_fl_isoforms(self):
 
  transcript_gene = self.select_reference_gene(intron_path, transcript_range, transcript_strand)
  if transcript_gene is None:
- transcript_gene = (GraphBasedModelConstructor.novel_gene_prefix + self.gene_info.chr_id +
+ transcript_gene = (TranscriptNaming.novel_gene_prefix + self.gene_info.chr_id +
  "_" + str(self.get_transcript_id()))
  elif transcript_strand == '.':
  transcript_strand = self.gene_info.gene_strands[transcript_gene]
 
  if all(intron in self.known_introns for intron in intron_path):
  transcript_type = TranscriptModelType.novel_in_catalog
- id_suffix = self.nic_transcript_suffix
+ id_suffix = TranscriptNaming.nic_transcript_suffix
  else:
  transcript_type = TranscriptModelType.novel_not_in_catalog
- id_suffix = self.nnic_transcript_suffix
+ id_suffix = TranscriptNaming.nnic_transcript_suffix
 
  new_model = TranscriptModel(self.gene_info.chr_id, transcript_strand,
  new_transcript_id + ".%s" % self.gene_info.chr_id + id_suffix,
@@ -644,11 +641,11 @@ def generate_monoexon_from_clustered(self, clustered_reads, forward=True):
 
  strand = '+' if forward else '-'
  coordinates = (five_prime_pos, three_prime_pos) if forward else (three_prime_pos, five_prime_pos)
- new_transcript_id = self.transcript_prefix + str(self.get_transcript_id())
- transcript_gene = (GraphBasedModelConstructor.novel_gene_prefix + self.gene_info.chr_id +
+ new_transcript_id = TranscriptNaming.transcript_prefix + str(self.get_transcript_id())
+ transcript_gene = (TranscriptNaming.novel_gene_prefix + self.gene_info.chr_id +
  "_" + str(self.get_transcript_id()))
  transcript_type = TranscriptModelType.novel_not_in_catalog
- id_suffix = self.nnic_transcript_suffix
+ id_suffix = TranscriptNaming.nnic_transcript_suffix
 
  is_valid = True
  half_len = interval_len(coordinates) / 2

src/id_policy.py

@@ -3,9 +3,9 @@
 # # All Rights Reserved
 # See file LICENSE for details.
 ############################################################################
+import threading
 
-
-from .graph_based_model_construction import GraphBasedModelConstructor
+from src.common import TranscriptNaming
 
 
 class SimpleIDDistributor(object):
@@ -25,7 +25,7 @@ def __init__(self, genedb, chr_id):
  return
 
  for g in genedb.region(seqid=chr_id, start=1, featuretype="gene"):
- if g.id.startswith(GraphBasedModelConstructor.novel_gene_prefix):
+ if g.id.startswith(TranscriptNaming.novel_gene_prefix):
  try:
  gene_num = int(g.id.split("_")[-1])
  self.forbidden_ids.add(gene_num)
@@ -34,9 +34,9 @@ def __init__(self, genedb, chr_id):
  except ValueError:
  pass
 
- transcript_num_start_pos = len(GraphBasedModelConstructor.transcript_prefix)
+ transcript_num_start_pos = len(TranscriptNaming.transcript_prefix)
  for t in genedb.region(seqid=chr_id, start=1, featuretype=("transcript", "mRNA")):
- if t.id.startswith(GraphBasedModelConstructor.transcript_prefix):
+ if t.id.startswith(TranscriptNaming.transcript_prefix):
  try:
  transcript_num = int(t.id.split(".")[0][transcript_num_start_pos:])
  self.forbidden_ids.add(transcript_num)
@@ -78,3 +78,14 @@ def get_id(self, chr_id, feature, strand):
  feature_id = self.id_dict[feature_tuple]
 
  return feature_id
+
+
+class AtomicIDDistributor(object):
+ def __init__(self):
+ self.value = 0
+ self._lock = threading.Lock()
+
+ def increment(self):
+ with self._lock:
+ self.value += 1
+ return self.value

src/isoform_assignment.py

@@ -7,7 +7,8 @@
 
 import logging
 from enum import Enum, unique
-from src.common import AtomicIDDistributor, junctions_from_blocks
+from src.common import junctions_from_blocks
+from src.id_policy import SimpleIDDistributor
 from src.serialization import *
 from src.polya_finder import PolyAInfo
 
@@ -619,7 +620,7 @@ def serialize(self, outfile):
 
 
 class ReadAssignment:
- assignment_id_generator = AtomicIDDistributor()
+ assignment_id_generator = SimpleIDDistributor()
 
  def __init__(self, read_id, assignment_type, match=None):
  self.assignment_id = ReadAssignment.assignment_id_generator.increment()