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Source code for galaxy.datatypes.assembly
"""
velvet datatypes
James E Johnson - University of Minnesota
for velvet assembler tool in galaxy
"""
from __future__ import absolute_import
import logging
import os
import re
import sys
from galaxy.datatypes import data
from galaxy.datatypes import sequence
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.text import Html
log = logging.getLogger(__name__)
[docs]class Amos(data.Text):
"""Class describing the AMOS assembly file """
edam_data = "data_0925"
edam_format = "format_3582"
file_ext = 'afg'
[docs] def sniff(self, filename):
# FIXME: this method will read the entire file.
# It should call get_headers() like other sniff methods.
"""
Determines whether the file is an amos assembly file format
Example::
{CTG
iid:1
eid:1
seq:
CCTCTCCTGTAGAGTTCAACCGA-GCCGGTAGAGTTTTATCA
.
qlt:
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
.
{TLE
src:1027
off:0
clr:618,0
gap:
250 612
.
}
}
"""
isAmos = False
try:
fh = open(filename)
while not isAmos:
line = fh.readline()
if not line:
break # EOF
line = line.strip()
if line: # first non-empty line
if line.startswith('{'):
if re.match(r'{(RED|CTG|TLE)$', line):
isAmos = True
fh.close()
except Exception:
pass
return isAmos
[docs]class Sequences(sequence.Fasta):
"""Class describing the Sequences file generated by velveth """
edam_data = "data_0925"
file_ext = 'sequences'
[docs] def sniff(self, filename):
"""
Determines whether the file is a velveth produced fasta format
The id line has 3 fields separated by tabs: sequence_name sequence_index category::
>SEQUENCE_0_length_35 1 1
GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT
>SEQUENCE_1_length_35 2 1
CGACGAATGACAGGTCACGAATTTGGCGGGGATTA
"""
try:
fh = open(filename)
while True:
line = fh.readline()
if not line:
break # EOF
line = line.strip()
if line: # first non-empty line
if line.startswith('>'):
if not re.match(r'>[^\t]+\t\d+\t\d+$', line):
break
# The next line.strip() must not be '', nor startwith '>'
line = fh.readline().strip()
if line == '' or line.startswith('>'):
break
return True
else:
break # we found a non-empty line, but it's not a fasta header
fh.close()
except Exception:
pass
return False
[docs]class Roadmaps(data.Text):
"""Class describing the Sequences file generated by velveth """
edam_format = "format_2561"
file_ext = 'roadmaps'
[docs] def sniff(self, filename):
"""
Determines whether the file is a velveth produced RoadMap::
142858 21 1
ROADMAP 1
ROADMAP 2
...
"""
try:
fh = open(filename)
while True:
line = fh.readline()
if not line:
break # EOF
line = line.strip()
if line: # first non-empty line
if not re.match(r'\d+\t\d+\t\d+$', line):
break
# The next line.strip() should be 'ROADMAP 1'
line = fh.readline().strip()
if not re.match(r'ROADMAP \d+$', line):
break
return True
else:
break # we found a non-empty line, but it's not a fasta header
fh.close()
except Exception:
pass
return False
[docs]class Velvet(Html):
MetadataElement(name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True)
MetadataElement(name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True)
MetadataElement(name="long_reads", desc="has long reads", default="False", readonly=False, set_in_upload=True)
MetadataElement(name="short2_reads", desc="has 2nd short reads", default="False", readonly=False, set_in_upload=True)
composite_type = 'auto_primary_file'
allow_datatype_change = False
file_ext = 'velvet'
[docs] def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False)
self.add_composite_file('Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False)
self.add_composite_file('Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False)
[docs] def generate_primary_file(self, dataset=None):
log.debug("Velvet log info %s %s" % ('JJ generate_primary_file', dataset))
rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
fn = composite_name
log.debug("Velvet log info %s %s %s" % ('JJ generate_primary_file', fn, composite_file))
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
if composite_file.get('description'):
rval.append('<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text))
else:
rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text))
rval.append('</ul></div></html>')
return "\n".join(rval)
[docs] def regenerate_primary_file(self, dataset):
"""
cannot do this until we are setting metadata
"""
log.debug("Velvet log info %s" % 'JJ regenerate_primary_file')
gen_msg = ''
try:
efp = dataset.extra_files_path
log_path = os.path.join(efp, 'Log')
f = open(log_path, 'r')
log_content = f.read(1000)
f.close()
log_msg = re.sub('/\S*/', '', log_content)
log.debug("Velveth log info %s" % log_msg)
paired_end_reads = re.search('-(short|long)Paired', log_msg) is not None
dataset.metadata.paired_end_reads = paired_end_reads
long_reads = re.search('-long', log_msg) is not None
dataset.metadata.long_reads = long_reads
short2_reads = re.search('-short(Paired)?2', log_msg) is not None
dataset.metadata.short2_reads = short2_reads
dataset.info = re.sub('.*velveth \S+', 'hash_length', re.sub('\n', ' ', log_msg))
if paired_end_reads:
gen_msg = gen_msg + ' Paired-End Reads'
if long_reads:
gen_msg = gen_msg + ' Long Reads'
if len(gen_msg) > 0:
gen_msg = 'Uses: ' + gen_msg
except Exception:
log.debug("Velveth could not read Log file in %s" % efp)
log.debug("Velveth log info %s" % gen_msg)
rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
# rval.append('<div>Generated:<p/><code> %s </code></div>' %(re.sub('\n','<br>',log_msg)))
rval.append('<div>Generated:<p/> %s </div>' % (gen_msg))
rval.append('<div>Velveth dataset:<p/><ul>')
for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
fn = composite_name
log.debug("Velvet log info %s %s %s" % ('JJ regenerate_primary_file', fn, composite_file))
if re.search('Log', fn) is None:
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
if composite_file.get('description'):
rval.append('<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text))
else:
rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text))
rval.append('</ul></div></html>')
with open(dataset.file_name, 'w') as f:
f.write("\n".join(rval))
f.write('\n')
[docs] def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
self.regenerate_primary_file(dataset)
if __name__ == '__main__':
import doctest
doctest.testmod(sys.modules[__name__])