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Psl.py
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Psl.py
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import logging
import os
import tempfile
# Internal dependencies
from Datatype import Datatype
from util import subtools
class Psl(Datatype):
def __init__(self, input_psl_path, data_psl):
super(Psl, self).__init__()
self.track = None
self.input_psl_path = input_psl_path
self.name_psl = data_psl["name"]
self.priority = data_psl["order_index"]
self.track_color = data_psl["track_color"]
# TODO: Think about how to avoid repetition of the group_name everywhere
self.group_name = data_psl["group_name"]
# Temporary files
unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
# Get the bed12+12 with pslToBigPsl
subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
# Sort the formatted psl into sorted_bed_formatted_psl_file
subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
# Get the binary indexed bigPsl with bedToBigBed
trackName = "".join((self.name_psl, ".bb"))
auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
logging.debug("Hello")
with open(my_big_psl_file_path, 'w') as big_psl_file:
subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
self.chromSizesFile.name,
big_psl_file.name,
autoSql=auto_sql_option,
typeOption='bed12+12',
tab=True)
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
long_label=self.name_psl,
track_type='bigPsl', visibility='dense',
priority=self.priority,
track_file=my_big_psl_file_path,
track_color=self.track_color,
group_name=self.group_name)
print("- BigPsl %s created" % self.name_psl)