import os
import re
+__docformat__ = "restructredtext en"
+
# map eland_result.txt sense
sense_map = { 'F': '+', 'R': '-'}
sense_color = { 'F': '0,0,255', 'R': '255,255,0' }
-def write_bed_header(outstream, name, description):
+def create_bed_header(name, description):
"""
Produce the headerline for a bedfile
"""
if description is None: description = "eland result file"
bed_header = 'track name="%s" description="%s" visibility=4 itemRgb="ON"'
bed_header += os.linesep
- outstream.write(bed_header % (name, description))
+ return bed_header
def make_bed_from_eland_stream(instream, outstream, name, description, chromosome_prefix='chr'):
"""
read an eland result file from instream and write a bedfile to outstream
+
+ :Parameters:
+ - `instream`: stream containing the output from eland
+ - `outstream`: stream to write the bed file too
+ - `name`: name of bed-file (must be unique)
+ - `description`: longer description of the bed file
+ - `chromosome_prefix`: restrict output lines to fasta records that start with this pattern
+ """
+ for line in make_bed_from_eland_generator(instream, name, description, chromosome_prefix):
+ outstream.write(line)
+
+def make_bed_from_eland_generator(instream, name, description, chromosome_prefix='chr'):
+ """
+ read an eland result file from instream and write a bedfile to outstream
+
+ :Parameters:
+ - `instream`: stream containing the output from eland
+ - `name`: name of bed-file (must be unique)
+ - `description`: longer description of the bed file
+ - `chromosome_prefix`: restrict output lines to fasta records that start with this pattern
+
+ :Return: generator which yields lines of bedfile
"""
# indexes into fields in eland_result.txt file
SEQ = 1
START = 7
SENSE = 8
- write_bed_header(outstream, name, description)
+ yield create_bed_header(name, description)
prefix_len = len(chromosome_prefix)
for line in instream:
# strip off filename extension
chromosome = fields[CHR].split('.')[0]
- outstream.write('%s %s %d read 0 %s - - %s%s' % (
+ yield '%s %s %d read 0 %s - - %s%s' % (
chromosome,
start,
stop,
sense_map[fields[SENSE]],
sense_color[fields[SENSE]],
os.linesep
- ))
-
+ )
def make_bed_from_multi_eland_stream(
instream,
max_reads=255
):
"""
- read a multi eland stream and write a bedfile
+ read a multi eland result file from instream and write the bedfile to outstream
+
+ :Parameters:
+ - `instream`: stream containing the output from eland
+ - `outstream`: stream to write the bed file too
+ - `name`: name of bed-file (must be unique)
+ - `description`: longer description of the bed file
+ - `chromosome_prefix`: restrict output lines to fasta records that start with this pattern
+ - `max_reads`: maximum number of reads to write to bed stream
"""
- write_bed_header(outstream, name, description)
- parse_multi_eland(instream, outstream, chr_prefix, max_reads)
-
-def parse_multi_eland(instream, outstream, chr_prefix, max_reads=255):
+ for lane in make_bed_from_multi_eland_generator(instream, name, description, chr_prefix, max_reads):
+ oustream.write(lane)
+def make_bed_from_multi_eland_generator(instream, name, description, chr_prefix, max_reads=255):
loc_pattern = '(?P<fullloc>(?P<start>[0-9]+)(?P<dir>[FR])(?P<count>[0-9]+))'
other_pattern = '(?P<chr>[^:,]+)'
split_re = re.compile('(%s|%s)' % (loc_pattern, other_pattern))
+ yield create_bed_header(name, description)
for line in instream:
rec = line.split()
if len(rec) > 3:
if reported_reads <= max_reads:
for cur_chr, start, stop, strand, color in read_list:
reported_reads += 1
- outstream.write('%s %d %d read 0 %s - - %s%s' % (
+ yield '%s %d %d read 0 %s - - %s%s' % (
cur_chr,
start,
stop,
sense_map[orientation],
sense_color[orientation],
os.linesep
- ))
+ )
-def make_description(database, flowcell_id, lane):
+def make_description(flowcell_id, lane):
"""
- compute a bedfile name and description from the fctracker database
+ compute a bedfile name and description from the django database
"""
- from htsworkflow.util.fctracker import fctracker
+ from htsworkflow.frontend.experiments import models as experiments
- fc = fctracker(database)
- cells = fc._get_flowcells("where flowcell_id='%s'" % (flowcell_id))
- if len(cells) != 1:
- raise RuntimeError("couldn't find flowcell id %s" % (flowcell_id))
lane = int(lane)
if lane < 1 or lane > 8:
raise RuntimeError("flowcells only have lanes 1-8")
- name = "%s-%s" % (flowcell_id, lane)
+ cell = experiments.FlowCell.objects.get(flowcell_id=flowcell_id)
- cell_id, cell = cells.items()[0]
- assert cell_id == flowcell_id
+ name = "%s-%s" % (flowcell_id, lane)
- cell_library_id = cell['lane_%d_library_id' %(lane,)]
- cell_library = cell['lane_%d_library' %(lane,)]
- description = "%s-%s" % (cell_library['library_name'], cell_library_id)
+ cell_library = getattr(cell, 'lane_%d_library' %(lane,))
+ cell_library_id = cell_library.library_id
+ description = "%s-%s" % (cell_library.library_name, cell_library_id)
return name, description
projects / htsworkflow.git / blobdiff