# Path: grit/merge.py
# LINKAGE_CLUSTER_GAP = 500
# def build_merged_transcript(gene_id, clustered_transcripts):
# def reduce_internal_clustered_transcripts( 
#         internal_grpd_transcripts, gene_id, max_cluster_gap ):
# def reduce_gene_clustered_transcripts(
#         genes, new_gene_id,
#         min_upper_fpkm=None, 
#         max_intrasample_fpkm_ratio=None, 
#         max_intersample_fpkm_ratio=None,
#         max_cluster_gap=50):
# def group_overlapping_genes(all_sources_and_pickled_gene_fnames):
# 
# Path: grit/lib/multiprocessing_utils.py
# class ThreadSafeFile( file ):
#     def __init__( *args ):
#         file.__init__( *args )
#         args[0].lock = multiprocessing.Lock()
# 
#     def write( self, string ):
#         with self.lock:
#             file.write( self, string )
#             self.flush()
# 
# Path: grit/files/gtf.py
# def load_multiple_gtfs_into_pickled_files(fnames):
#     # load all the gtfs
#     import multiprocessing
#     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)
#             os._exit(0)
#         else:
#             pids.append(pid)
#     
#     for pid in pids:
#         os.waitpid(pid, 0)
#     del all_genes_and_fnames_lock
#     all_genes_and_fnames = list(all_genes_and_fnames)
#     manager.shutdown()
#     
#     return all_genes_and_fnames


import os, sys
import cPickle as pickle
import multiprocessing
import grit.config as config
    import argparse
from grit.merge import (
    group_overlapping_genes, 
    reduce_gene_clustered_transcripts, 
    fix_chrm_name_for_ucsc)
from grit.lib.multiprocessing_utils import ThreadSafeFile
from grit.files.gtf import load_multiple_gtfs_into_pickled_files
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

GRIT is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with GRIT.  If not, see <http://www.gnu.org/licenses/>.
"""




def parse_arguments():
    desc = 'Merge transcripts.'
    parser = argparse.ArgumentParser(description=desc)    
    parser.add_argument(
        "gtfs", type=file, nargs="+",
        help='GTF file contraining transcripts. (i.e. from build_transcripts)' )
    
    parser.add_argument(
        '--out-fname', '-o', 
        type=lambda fname: ThreadSafeFile(fname, 'w'), 
        default=sys.stdout,
        help='Output file. default: stdout')
    
    parser.add_argument(
        '--out-sources-fname', 

# Path: grit/merge.py
# LINKAGE_CLUSTER_GAP = 500
# def build_merged_transcript(gene_id, clustered_transcripts):
# def reduce_internal_clustered_transcripts( 
#         internal_grpd_transcripts, gene_id, max_cluster_gap ):
# def reduce_gene_clustered_transcripts(
#         genes, new_gene_id,
#         min_upper_fpkm=None, 
#         max_intrasample_fpkm_ratio=None, 
#         max_intersample_fpkm_ratio=None,
#         max_cluster_gap=50):
# def group_overlapping_genes(all_sources_and_pickled_gene_fnames):
# 
# Path: grit/lib/multiprocessing_utils.py
# class ThreadSafeFile( file ):
#     def __init__( *args ):
#         file.__init__( *args )
#         args[0].lock = multiprocessing.Lock()
# 
#     def write( self, string ):
#         with self.lock:
#             file.write( self, string )
#             self.flush()
# 
# Path: grit/files/gtf.py
# def load_multiple_gtfs_into_pickled_files(fnames):
#     # load all the gtfs
#     import multiprocessing
#     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)
#             os._exit(0)
#         else:
#             pids.append(pid)
#     
#     for pid in pids:
#         os.waitpid(pid, 0)
#     del all_genes_and_fnames_lock
#     all_genes_and_fnames = list(all_genes_and_fnames)
#     manager.shutdown()
#     
#     return all_genes_and_fnames


# Path: bin/merge_transcripts.py
import os, sys
import cPickle as pickle
import multiprocessing
import grit.config as config
    import argparse
from grit.merge import (
    group_overlapping_genes, 
    reduce_gene_clustered_transcripts, 
    fix_chrm_name_for_ucsc)
from grit.lib.multiprocessing_utils import ThreadSafeFile
from grit.files.gtf import load_multiple_gtfs_into_pickled_files

the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

GRIT is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with GRIT.  If not, see <http://www.gnu.org/licenses/>.
"""




def parse_arguments():
    desc = 'Merge transcripts.'
    parser = argparse.ArgumentParser(description=desc)    
    parser.add_argument(
        "gtfs", type=file, nargs="+",
        help='GTF file contraining transcripts. (i.e. from build_transcripts)' )
    
    parser.add_argument(
        '--out-fname', '-o', 
        type=lambda fname: ThreadSafeFile(fname, 'w'), 
        default=sys.stdout,
        help='Output file. default: stdout')
    
    parser.add_argument(
        '--out-sources-fname', 

        type=lambda fname: ThreadSafeFile(fname, 'w'),