# Path: grit/transcript.py
# VERBOSE = False
# def partition_coding_and_utr_segments( exons, cds_start, cds_stop ):
#     def mod_external_bndrys( exons, lower_bnd, upper_bnd ):
#     def __init__(self, id, name, 
#                  chrm, strand, start, stop, 
#                  transcripts, meta_data={}):
#     def find_nonoverlapping_boundaries( self ):
#     def write_to_file(self, ofname=None):
#     def find_transcribed_regions( self ):
#     def calc_bpkm(self, read_cov):
#     def extract_elements(self):
#     def __init__(self, trans_id, chrm, strand, exons, cds_region,
#                  gene_id, score=None, fpkm=None, fpk=None, 
#                  promoter=None, polya_region=None, coding_sequence=None,
#                  conf_lo=None, conf_hi=None, frac=None,
#                  gene_name=None, name=None):
#     def add_cds_region( self, cds_region, coding_sequence=None ):
#     def __hash__( self ):
#     def IB_key( self ):
#     def relative_pos( self, genome_coord ):
#     def genome_pos( self, trans_coord ):
#     def build_gtf_lines( self, meta_data, source='.'):
#         def build_lines_for_feature( exons, feature, is_CDS=False ):
#         def order(line):
#     def calc_length(self):
#     def build_tracking_line(self):
#     def find_promoter(self, inferred_promoter_length=50):
#     def find_polya_region(self, inferred_polya_region_length=20):
# class Gene( object ):
# class Transcript( object ):
# 
# Path: grit/config.py
# def log_statement(*args, **kwargs):
#     print args[0]
# 
# VERBOSE = None


import os, sys
import itertools
import tempfile
import gzip
import traceback
    import multiprocessing
from collections import namedtuple, defaultdict
from ..transcript import Gene, Transcript, GenomicInterval
from reads import clean_chr_name
from tracking import load_expression_tracking_data
from ..config import log_statement, VERBOSE
            gene.write_to_file(ofname)
            pickled_gene_fnames.append( ofname )
        except StopIteration:
            return pickled_gene_fnames

def load_gtf_and_expression_data_into_pickled_files(fname):
    sample_type = os.path.basename(fname).split('.')[0]
    expression_fnames = [ 
            os.path.join(os.path.dirname(fname), f) 
            for f in os.listdir(os.path.dirname(fname)) 
            if os.path.basename(f).startswith(sample_type)
            and os.path.basename(f).endswith("expression_tracking") ]
    pickled_gene_fnames = load_gtf_into_pickled_files(
            fname, expression_fnames=expression_fnames)
    return pickled_gene_fnames

def load_multiple_gtfs_into_pickled_files(fnames):
    # load all the gtfs
    manager = multiprocessing.Manager()
    all_genes_and_fnames = manager.list()
    all_genes_and_fnames_lock = multiprocessing.Lock()
    pids = []
    for fname in fnames:
        pid = os.fork()
        if pid == 0:
            log_statement("Loading %s" % fname)
            pickled_gene_fnames = load_gtf_and_expression_data_into_pickled_files(
                fname)
            with all_genes_and_fnames_lock:
                all_genes_and_fnames.append((fname, pickled_gene_fnames))

# Path: grit/transcript.py
# VERBOSE = False
# def partition_coding_and_utr_segments( exons, cds_start, cds_stop ):
#     def mod_external_bndrys( exons, lower_bnd, upper_bnd ):
#     def __init__(self, id, name, 
#                  chrm, strand, start, stop, 
#                  transcripts, meta_data={}):
#     def find_nonoverlapping_boundaries( self ):
#     def write_to_file(self, ofname=None):
#     def find_transcribed_regions( self ):
#     def calc_bpkm(self, read_cov):
#     def extract_elements(self):
#     def __init__(self, trans_id, chrm, strand, exons, cds_region,
#                  gene_id, score=None, fpkm=None, fpk=None, 
#                  promoter=None, polya_region=None, coding_sequence=None,
#                  conf_lo=None, conf_hi=None, frac=None,
#                  gene_name=None, name=None):
#     def add_cds_region( self, cds_region, coding_sequence=None ):
#     def __hash__( self ):
#     def IB_key( self ):
#     def relative_pos( self, genome_coord ):
#     def genome_pos( self, trans_coord ):
#     def build_gtf_lines( self, meta_data, source='.'):
#         def build_lines_for_feature( exons, feature, is_CDS=False ):
#         def order(line):
#     def calc_length(self):
#     def build_tracking_line(self):
#     def find_promoter(self, inferred_promoter_length=50):
#     def find_polya_region(self, inferred_polya_region_length=20):
# class Gene( object ):
# class Transcript( object ):
# 
# Path: grit/config.py
# def log_statement(*args, **kwargs):
#     print args[0]
# 
# VERBOSE = None


# Path: grit/files/gtf.py
import os, sys
import itertools
import tempfile
import gzip
import traceback
    import multiprocessing
from collections import namedtuple, defaultdict
from ..transcript import Gene, Transcript, GenomicInterval
from reads import clean_chr_name
from tracking import load_expression_tracking_data
from ..config import log_statement, VERBOSE

            gene.write_to_file(ofname)
            pickled_gene_fnames.append( ofname )
        except StopIteration:
            return pickled_gene_fnames

def load_gtf_and_expression_data_into_pickled_files(fname):
    sample_type = os.path.basename(fname).split('.')[0]
    expression_fnames = [ 
            os.path.join(os.path.dirname(fname), f) 
            for f in os.listdir(os.path.dirname(fname)) 
            if os.path.basename(f).startswith(sample_type)
            and os.path.basename(f).endswith("expression_tracking") ]
    pickled_gene_fnames = load_gtf_into_pickled_files(
            fname, expression_fnames=expression_fnames)
    return pickled_gene_fnames

def load_multiple_gtfs_into_pickled_files(fnames):
    # load all the gtfs
    manager = multiprocessing.Manager()
    all_genes_and_fnames = manager.list()
    all_genes_and_fnames_lock = multiprocessing.Lock()
    pids = []
    for fname in fnames:
        pid = os.fork()
        if pid == 0:
            log_statement("Loading %s" % fname)
            pickled_gene_fnames = load_gtf_and_expression_data_into_pickled_files(
                fname)
            with all_genes_and_fnames_lock:
                all_genes_and_fnames.append((fname, pickled_gene_fnames))

            log_statement("FINISHED Loading %s" % fname)