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Source code for galaxy.datatypes.assembly
"""
velvet datatypes
James E Johnson - University of Minnesota
for velvet assembler tool in galaxy
"""
import logging
import os
import re
from galaxy.datatypes import (
data,
sequence,
)
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import (
DatasetProtocol,
HasExtraFilesAndMetadata,
)
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
FilePrefix,
)
from galaxy.datatypes.text import Html
log = logging.getLogger(__name__)
[docs]@build_sniff_from_prefix
class Amos(data.Text):
"""Class describing the AMOS assembly file"""
edam_data = "data_0925"
edam_format = "format_3582"
file_ext = "afg"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
"""
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
.
}
}
"""
for line in file_prefix.line_iterator():
if not line:
break # EOF
line = line.strip()
if line: # first non-empty line
if line.startswith("{"):
if re.match(r"{(RED|CTG|TLE)$", line):
return True
return False
[docs]@build_sniff_from_prefix
class Sequences(sequence.Fasta):
"""Class describing the Sequences file generated by velveth"""
edam_data = "data_0925"
file_ext = "sequences"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
"""
Determines whether the file is a velveth produced fasta format
The id line has 3 fields separated by tabs: sequence_name sequence_index category::
>SEQUENCE_0_length_35 1 1
GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT
>SEQUENCE_1_length_35 2 1
CGACGAATGACAGGTCACGAATTTGGCGGGGATTA
"""
fh = file_prefix.string_io()
for line in fh:
line = line.strip()
if line: # first non-empty line
if line.startswith(">"):
if not re.match(r">[^\t]+\t\d+\t\d+$", line):
return False
# The next line.strip() must not be '', nor startwith '>'
line = fh.readline().strip()
if line == "" or line.startswith(">"):
return False
return True
else:
return False
return False
[docs]@build_sniff_from_prefix
class Roadmaps(data.Text):
"""Class describing the Sequences file generated by velveth"""
edam_format = "format_2561"
file_ext = "roadmaps"
[docs] def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
"""
Determines whether the file is a velveth produced RoadMap::
142858 21 1
ROADMAP 1
ROADMAP 2
...
"""
fh = file_prefix.string_io()
for line in fh:
line = line.strip()
if line: # first non-empty line
if not re.match(r"\d+\t\d+\t\d+$", line):
return False
# The next line.strip() should be 'ROADMAP 1'
line = fh.readline().strip()
return bool(re.match(r"ROADMAP \d+$", line))
else:
return False # we found a non-empty line, but it's not a fasta header
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"
file_ext = "velvet"
[docs] def __init__(self, **kwd):
super().__init__(**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: HasExtraFilesAndMetadata) -> str:
log.debug(f"Velvet log info 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(f"Velvet log info JJ generate_primary_file {fn} {composite_file}")
opt_text = ""
if composite_file.optional:
opt_text = " (optional)"
if composite_file.get("description"):
rval.append(
f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
)
else:
rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
rval.append("</ul></div></html>")
return "\n".join(rval)
[docs] def regenerate_primary_file(self, dataset: DatasetProtocol) -> None:
"""
cannot do this until we are setting metadata
"""
log.debug(f"Velvet log info {'JJ regenerate_primary_file'}")
gen_msg = ""
try:
efp = dataset.extra_files_path
log_path = os.path.join(efp, "Log")
with open(log_path) as f:
log_content = f.read(1000)
log_msg = re.sub(r"/\S*/", "", log_content)
log.debug(f"Velveth log info {log_msg}")
paired_end_reads = re.search(r"-(short|long)Paired", log_msg) is not None
dataset.metadata.paired_end_reads = paired_end_reads
long_reads = re.search(r"-long", log_msg) is not None
dataset.metadata.long_reads = long_reads
short2_reads = re.search(r"-short(Paired)?2", log_msg) is not None
dataset.metadata.short2_reads = short2_reads
dataset.info = re.sub(r".*velveth \S+", "hash_length", re.sub(r"\n", " ", log_msg))
if paired_end_reads:
gen_msg = f"{gen_msg} Paired-End Reads"
if long_reads:
gen_msg = f"{gen_msg} Long Reads"
if len(gen_msg) > 0:
gen_msg = f"Uses: {gen_msg}"
except Exception:
log.debug(f"Velveth could not read Log file in {efp}")
log.debug(f"Velveth log info {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(f"<div>Generated:<p/> {gen_msg} </div>")
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(f"Velvet log info 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(
f"<li><a href=\"{fn}\" type=\"text/plain\">{fn} ({composite_file.get('description')})</a>{opt_text}</li>"
)
else:
rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
rval.append("</ul></div></html>")
with open(dataset.get_file_name(), "w") as f:
f.write("\n".join(rval))
f.write("\n")
[docs] def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
Html.set_meta(self, dataset, overwrite=overwrite, **kwd)
self.regenerate_primary_file(dataset)