from mrjob.job import MRJob
from odetta.utils import model_parser
splat_model = model_parser([
('reference', ''),
('flanks', ''),
('a_length', 0),
('b_length', 0),
('intron_length', 0),
('a_start', 0),
('a_end', 0),
('b_start', 0),
('b_end', 0),
('sequence', ''),
('read_count', 0),
('read_IDs', ''),
])
class Splat(MRJob):
"""
Parse a Splat formatted line.
"""
def parse_line(self, line):
data = splat_model(line.split('\t'))
if data['a_start'] <= data['b_start']:
data['start'] = data['a_start']
data['end'] = data['b_end']
from mrjob.job import MRJob
from odetta.utils import model_parser
sam_model = model_parser([
('ID', ''),
('flag', 0),
('reference', ''),
('start', 0),
('map_quality', 0),
('CIGAR', ''),
('rnext', ''),
('pnext', ''),
('tlen', ''),
('sequence', ''),
('quality', ''),
])
class SAM(MRJob):
"""
Parse a SAM formatted file.
http://samtools.sourceforge.net/samtools.shtml#5
"""
def configure_options(self):
"""Define command-line options."""
super(SAM, self).configure_options()
self.add_passthrough_option('--type',
default='SAM',
from mrjob.job import MRJob
from odetta.utils import model_parser
splat_model = model_parser([
('reference', ''),
('flanks', ''),
('a_length', 0),
('b_length', 0),
('intron_length', 0),
('a_start', 0),
('a_end', 0),
('b_start', 0),
('b_end', 0),
('sequence', ''),
('read_count', 0),
('read_IDs', ''),
])
class Splat(MRJob):
"""
Parse a Splat formatted line.
"""
def parse_line(self, line):
data = splat_model(line.split('\t'))
if data['a_start'] <= data['b_start']:
data['start'] = data['a_start']
from mrjob.job import MRJob
from odetta.utils import model_parser
bowtie_model = model_parser([
('ID', ''),
('strand', '+'),
('reference', ''),
('start', 0),
('sequence', ''),
])
#TODO unit test
class Bowtie(MRJob):
"""
Parse a bowtie-formatted file. This is a very specific format,
output with --suppress 6,7,8
http://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output
"""
def configure_options(self):
"""Define command-line options."""
super(Bowtie, self).configure_options()
self.add_passthrough_option('--type', default='bowtie',
help="set the 'type' attribute")
from mrjob.job import MRJob
from odetta.utils import model_parser
sam_model = model_parser(
[
("ID", ""),
("flag", 0),
("reference", ""),
("start", 0),
("map_quality", 0),
("CIGAR", ""),
("rnext", ""),
("pnext", ""),
("tlen", ""),
("sequence", ""),
("quality", ""),
]
)
class SAM(MRJob):
"""
Parse a SAM formatted file.
http://samtools.sourceforge.net/samtools.shtml#5
"""
def configure_options(self):
