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Source code for galaxy.datatypes.sequence

"""
Sequence classes
"""

import json
import logging
import os
import re
import string
import subprocess
import sys
from cgi import escape
from itertools import islice

import bx.align.maf

from galaxy import util
from galaxy.datatypes import metadata
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import (
    get_headers,
    iter_headers
)
from galaxy.util import (
    compression_utils,
    nice_size
)
from galaxy.util.checkers import (
    is_bz2,
    is_gzip
)

from galaxy.util.image_util import check_image_type

from . import data

if sys.version_info > (3,):
    long = int

log = logging.getLogger(__name__)

SNIFF_COMPRESSED_FASTQS = os.environ.get("GALAXY_ENABLE_BETA_COMPRESSED_FASTQ_SNIFFING", "0") == "1"


[docs]class SequenceSplitLocations(data.Text): """ Class storing information about a sequence file composed of multiple gzip files concatenated as one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. The format of the file is JSON:: { "sections" : [ { "start" : "x", "end" : "y", "sequences" : "z" }, ... ]} """ file_ext = "fqtoc"
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: try: parsed_data = json.load(open(dataset.file_name)) # dataset.peek = json.dumps(data, sort_keys=True, indent=4) dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) dataset.blurb = '%d sections' % len(parsed_data['sections']) except Exception: dataset.peek = 'Not FQTOC file' dataset.blurb = 'Not FQTOC file' else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): if os.path.getsize(filename) < 50000: try: data = json.load(open(filename)) sections = data['sections'] for section in sections: if 'start' not in section or 'end' not in section or 'sequences' not in section: return False return True except: pass return False
[docs]class Sequence(data.Text): """Class describing a sequence""" edam_data = "data_2044" """Add metadata elements""" MetadataElement(name="sequences", default=0, desc="Number of sequences", readonly=True, visible=False, optional=True, no_value=0)
[docs] def set_meta(self, dataset, **kwd): """ Set the number of sequences and the number of data lines in dataset. """ data_lines = 0 sequences = 0 for line in open(dataset.file_name): line = line.strip() if line and line.startswith('#'): # We don't count comment lines for sequence data types continue if line and line.startswith('>'): sequences += 1 data_lines += 1 else: data_lines += 1 dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) if dataset.metadata.sequences: dataset.blurb = "%s sequences" % util.commaify(str(dataset.metadata.sequences)) else: dataset.blurb = nice_size(dataset.get_size()) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def get_sequences_per_file(total_sequences, split_params): if split_params['split_mode'] == 'number_of_parts': # legacy basic mode - split into a specified number of parts parts = int(split_params['split_size']) sequences_per_file = [total_sequences / parts for i in range(parts)] for i in range(total_sequences % parts): sequences_per_file[i] += 1 elif split_params['split_mode'] == 'to_size': # loop through the sections and calculate the number of sequences chunk_size = long(split_params['split_size']) rem = total_sequences % chunk_size sequences_per_file = [chunk_size for i in range(total_sequences / chunk_size)] # TODO: Should we invest the time in a better way to handle small remainders? if rem > 0: sequences_per_file.append(rem) else: raise Exception('Unsupported split mode %s' % split_params['split_mode']) return sequences_per_file
get_sequences_per_file = staticmethod(get_sequences_per_file)
[docs] def do_slow_split(cls, input_datasets, subdir_generator_function, split_params): # count the sequences so we can split # TODO: if metadata is present, take the number of lines / 4 if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None: total_sequences = input_datasets[0].metadata.sequences else: with compression_utils.get_fileobj(input_datasets[0].file_name) as in_file: total_sequences = long(0) for i, line in enumerate(in_file): total_sequences += 1 total_sequences /= 4 sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params) return cls.write_split_files(input_datasets, None, subdir_generator_function, sequences_per_file)
do_slow_split = classmethod(do_slow_split)
[docs] def do_fast_split(cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params): data = json.load(open(toc_file_datasets[0].file_name)) sections = data['sections'] total_sequences = long(0) for section in sections: total_sequences += long(section['sequences']) sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params) return cls.write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)
do_fast_split = classmethod(do_fast_split)
[docs] def write_split_files(cls, input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file): directories = [] def get_subdir(idx): if idx < len(directories): return directories[idx] dir = subdir_generator_function() directories.append(dir) return dir # we know how many splits and how many sequences in each. What remains is to write out instructions for the # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of # those instructions is delegated to scripts start_sequence = 0 for part_no in range(len(sequences_per_file)): dir = get_subdir(part_no) for ds_no in range(len(input_datasets)): ds = input_datasets[ds_no] base_name = os.path.basename(ds.file_name) part_path = os.path.join(dir, base_name) split_data = dict(class_name='%s.%s' % (cls.__module__, cls.__name__), output_name=part_path, input_name=ds.file_name, args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no])) if toc_file_datasets is not None: toc = toc_file_datasets[ds_no] split_data['args']['toc_file'] = toc.file_name f = open(os.path.join(dir, 'split_info_%s.json' % base_name), 'w') json.dump(split_data, f) f.close() start_sequence += sequences_per_file[part_no] return directories
write_split_files = classmethod(write_split_files)
[docs] def split(cls, input_datasets, subdir_generator_function, split_params): """Split a generic sequence file (not sensible or possible, see subclasses).""" if split_params is None: return None raise NotImplementedError("Can't split generic sequence files")
[docs] def get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count): """ Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of shell commands that will extract the parts necessary >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10) ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5) ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=20) ['dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz'] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=10) ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', '(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=10, sequence_count=10) ['dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20) ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] """ sections = toc_file['sections'] result = [] current_sequence = long(0) i = 0 # skip to the section that contains my starting sequence while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['sequences']): current_sequence += long(sections[i]['sequences']) i += 1 if i == len(sections): # bad input data! raise Exception('No FQTOC section contains starting sequence %s' % start_sequence) # These two variables act as an accumulator for consecutive entire blocks that # can be copied verbatim (without decompressing) start_chunk = long(-1) end_chunk = long(-1) copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s' while sequence_count > 0 and i < len(sections): # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the # right number of lines sequences = long(sections[i]['sequences']) skip_sequences = start_sequence - current_sequence sequences_to_extract = min(sequence_count, sequences - skip_sequences) start_copy = long(sections[i]['start']) end_copy = long(sections[i]['end']) if sequences_to_extract < sequences: if start_chunk > -1: result.append(copy_chunk_cmd % (start_chunk, end_chunk - start_chunk, input_name, output_name)) start_chunk = -1 # extract, unzip, trim, recompress result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' % (start_copy, end_copy - start_copy, input_name, skip_sequences * 4 + 1, sequences_to_extract * 4, output_name)) else: # whole section - add it to the start_chunk/end_chunk accumulator if start_chunk == -1: start_chunk = start_copy end_chunk = end_copy sequence_count -= sequences_to_extract start_sequence += sequences_to_extract current_sequence += sequences i += 1 if start_chunk > -1: result.append(copy_chunk_cmd % (start_chunk, end_chunk - start_chunk, input_name, output_name)) if sequence_count > 0: raise Exception('%s sequences not found in file' % sequence_count) return result
get_split_commands_with_toc = staticmethod(get_split_commands_with_toc)
[docs] def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): """ Does a brain-dead sequential scan & extract of certain sequences >>> Sequence.get_split_commands_sequential(True, './input.gz', './output.gz', start_sequence=0, sequence_count=10) ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > "./output.gz"'] >>> Sequence.get_split_commands_sequential(False, './input.fastq', './output.fastq', start_sequence=10, sequence_count=10) ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 > "./output.fastq"'] """ start_line = start_sequence * 4 line_count = sequence_count * 4 # TODO: verify that tail can handle 64-bit numbers if is_compressed: cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c' % (input_name, start_line + 1, line_count) else: cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s' % (start_line + 1, input_name, line_count) cmd += ' > "%s"' % output_name return [cmd]
get_split_commands_sequential = staticmethod(get_split_commands_sequential)
[docs]class Alignment(data.Text): """Class describing an alignment""" edam_data = "data_0863" """Add metadata elements""" MetadataElement(name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None)
[docs] def split(cls, input_datasets, subdir_generator_function, split_params): """Split a generic alignment file (not sensible or possible, see subclasses).""" if split_params is None: return None raise NotImplementedError("Can't split generic alignment files")
[docs]class Fasta(Sequence): """Class representing a FASTA sequence""" edam_format = "format_1929" file_ext = "fasta"
[docs] def sniff(self, filename): """ Determines whether the file is in fasta format A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml Rules for sniffing as True: We don't care about line length (other than empty lines). The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header. 'sequence data' here is loosely defined as non-empty lines which do not start with '>' This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data) Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta) This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta We will only check that the first purported sequence is correctly formatted. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'sequence.maf' ) >>> Fasta().sniff( fname ) False >>> fname = get_test_fname( 'sequence.fasta' ) >>> Fasta().sniff( fname ) True """ 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('>'): # The next line.strip() must not be '', nor startwith '>' line = fh.readline().strip() if line == '' or line.startswith('>'): break # If there is a third line, and it isn't a header line, it may not contain chars like '()[].' otherwise it's most likely a DotBracket file line = fh.readline() if not line.startswith('>') and re.search("[\(\)\[\]\.]", line): break return True else: break # we found a non-empty line, but it's not a fasta header fh.close() except: pass return False
[docs] def split(cls, input_datasets, subdir_generator_function, split_params): """Split a FASTA file sequence by sequence. Note that even if split_mode="number_of_parts", the actual number of sub-files produced may not match that requested by split_size. If split_mode="to_size" then split_size is treated as the number of FASTA records to put in each sub-file (not size in bytes). """ if split_params is None: return if len(input_datasets) > 1: raise Exception("FASTA file splitting does not support multiple files") input_file = input_datasets[0].file_name # Counting chunk size as number of sequences. if 'split_mode' not in split_params: raise Exception('Tool does not define a split mode') elif split_params['split_mode'] == 'number_of_parts': split_size = int(split_params['split_size']) log.debug("Split %s into %i parts..." % (input_file, split_size)) # if split_mode = number_of_parts, and split_size = 10, and # we know the number of sequences (say 1234), then divide by # by ten, giving ten files of approx 123 sequences each. if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences: # Galaxy has already counted/estimated the number batch_size = 1 + input_datasets[0].metadata.sequences // split_size cls._count_split(input_file, batch_size, subdir_generator_function) else: # OK, if Galaxy hasn't counted them, it may be a big file. # We're not going to count the records which would be slow # and a waste of disk IO time - instead we'll split using # the file size. chunk_size = os.path.getsize(input_file) // split_size cls._size_split(input_file, chunk_size, subdir_generator_function) elif split_params['split_mode'] == 'to_size': # Split the input file into as many sub-files as required, # each containing to_size many sequences batch_size = int(split_params['split_size']) log.debug("Split %s into batches of %i records..." % (input_file, batch_size)) cls._count_split(input_file, batch_size, subdir_generator_function) else: raise Exception('Unsupported split mode %s' % split_params['split_mode'])
split = classmethod(split) def _size_split(cls, input_file, chunk_size, subdir_generator_function): """Split a FASTA file into chunks based on size on disk. This does of course preserve complete records - it only splits at the start of a new FASTQ sequence record. """ log.debug("Attemping to split FASTA file %s into chunks of %i bytes" % (input_file, chunk_size)) f = open(input_file, "rU") part_file = None try: # Note if the input FASTA file has no sequences, we will # produce just one sub-file which will be a copy of it. part_dir = subdir_generator_function() part_path = os.path.join(part_dir, os.path.basename(input_file)) part_file = open(part_path, 'w') log.debug("Writing %s part to %s" % (input_file, part_path)) start_offset = 0 while True: offset = f.tell() line = f.readline() if not line: break if line[0] == ">" and offset - start_offset >= chunk_size: # Start a new sub-file part_file.close() part_dir = subdir_generator_function() part_path = os.path.join(part_dir, os.path.basename(input_file)) part_file = open(part_path, 'w') log.debug("Writing %s part to %s" % (input_file, part_path)) start_offset = f.tell() part_file.write(line) except Exception as e: log.error('Unable to size split FASTA file: %s' % str(e)) f.close() if part_file is not None: part_file.close() raise f.close() _size_split = classmethod(_size_split) def _count_split(cls, input_file, chunk_size, subdir_generator_function): """Split a FASTA file into chunks based on counting records.""" log.debug("Attemping to split FASTA file %s into chunks of %i sequences" % (input_file, chunk_size)) f = open(input_file, "rU") part_file = None try: # Note if the input FASTA file has no sequences, we will # produce just one sub-file which will be a copy of it. part_dir = subdir_generator_function() part_path = os.path.join(part_dir, os.path.basename(input_file)) part_file = open(part_path, 'w') log.debug("Writing %s part to %s" % (input_file, part_path)) rec_count = 0 while True: line = f.readline() if not line: break if line[0] == ">": rec_count += 1 if rec_count > chunk_size: # Start a new sub-file part_file.close() part_dir = subdir_generator_function() part_path = os.path.join(part_dir, os.path.basename(input_file)) part_file = open(part_path, 'w') log.debug("Writing %s part to %s" % (input_file, part_path)) rec_count = 1 part_file.write(line) part_file.close() except Exception as e: log.error('Unable to count split FASTA file: %s' % str(e)) f.close() if part_file is not None: part_file.close() raise f.close() _count_split = classmethod(_count_split)
[docs]class csFasta(Sequence): """ Class representing the SOLID Color-Space sequence ( csfasta ) """ edam_format = "format_3589" file_ext = "csfasta"
[docs] def sniff(self, filename): """ Color-space sequence: >2_15_85_F3 T213021013012303002332212012112221222112212222 >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'sequence.fasta' ) >>> csFasta().sniff( fname ) False >>> fname = get_test_fname( 'sequence.csfasta' ) >>> csFasta().sniff( fname ) True """ try: fh = open(filename) while True: line = fh.readline() if not line: break # EOF line = line.strip() if line and not line.startswith('#'): # first non-empty non-comment line if line.startswith('>'): line = fh.readline().strip() if line == '' or line.startswith('>'): break elif line[0] not in string.ascii_uppercase: return False elif len(line) > 1 and not re.search('^[\d.]+$', line[1:]): return False return True else: break # we found a non-empty line, but it's not a header fh.close() except: pass return False
[docs] def set_meta(self, dataset, **kwd): if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None dataset.metadata.sequences = None return return Sequence.set_meta(self, dataset, **kwd)
[docs]class BaseFastq (Sequence): """Base class for FastQ sequences""" edam_format = "format_1930" file_ext = "fastq"
[docs] def set_meta(self, dataset, **kwd): """ Set the number of sequences and the number of data lines in dataset. FIXME: This does not properly handle line wrapping """ if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None dataset.metadata.sequences = None return data_lines = 0 sequences = 0 seq_counter = 0 # blocks should be 4 lines long with compression_utils.get_fileobj(dataset.file_name) as in_file: for line in in_file: line = line.strip() if line and line.startswith('#') and not data_lines: # We don't count comment lines for sequence data types continue seq_counter += 1 data_lines += 1 if line and line.startswith('@'): if seq_counter >= 4: # count previous block # blocks should be 4 lines long sequences += 1 seq_counter = 1 if seq_counter >= 4: # count final block sequences += 1 dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences
[docs] def sniff(self, filename): """ Determines whether the file is in generic fastq format For details, see http://maq.sourceforge.net/fastq.shtml Note: There are three kinds of FASTQ files, known as "Sanger" (sometimes called "Standard"), Solexa, and Illumina These differ in the representation of the quality scores >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( '1.fastqsanger' ) >>> FastqSanger().sniff( fname ) True >>> fname = get_test_fname( '2.fastqsanger' ) >>> FastqSanger().sniff( fname ) True >>> fname = get_test_fname( '2.fastq' ) >>> Fastq().sniff( fname ) True >>> FastqSanger().sniff( fname ) False """ compressed = is_gzip(filename) or is_bz2(filename) if compressed and not isinstance(self, Binary): return False headers = iter_headers(filename, None, count=1000) # If this is a FastqSanger-derived class, then check to see if the base qualities match if isinstance(self, FastqSanger) or isinstance(self, FastqSangerGz) or isinstance(self, FastqSangerBz2): if not self.sangerQualities(headers): return False bases_regexp = re.compile("^[NGTAC]*") # check that first block looks like a fastq block try: headers = get_headers(filename, None, count=4) if len(headers) == 4 and headers[0][0] and headers[0][0][0] == "@" and headers[2][0] and headers[2][0][0] == "+" and headers[1][0]: # Check the sequence line, make sure it contains only G/C/A/T/N if not bases_regexp.match(headers[1][0]): return False return True return False except: return False
[docs] def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd): if preview: with compression_utils.get_fileobj(dataset.file_name) as fh: max_peek_size = 1000000 # 1 MB if os.stat(dataset.file_name).st_size < max_peek_size: mime = "text/plain" self._clean_and_set_mime_type(trans, mime) return fh.read() return trans.stream_template_mako("/dataset/large_file.mako", truncated_data=fh.read(max_peek_size), data=dataset) else: return Sequence.display_data(self, trans, dataset, preview, filename, to_ext, **kwd)
[docs] def split(cls, input_datasets, subdir_generator_function, split_params): """ FASTQ files are split on cluster boundaries, in increments of 4 lines """ if split_params is None: return None # first, see if there are any associated FQTOC files that will give us the split locations # if so, we don't need to read the files to do the splitting toc_file_datasets = [] for ds in input_datasets: tmp_ds = ds fqtoc_file = None while fqtoc_file is None and tmp_ds is not None: fqtoc_file = tmp_ds.get_converted_files_by_type('fqtoc') tmp_ds = tmp_ds.copied_from_library_dataset_dataset_association if fqtoc_file is not None: toc_file_datasets.append(fqtoc_file) if len(toc_file_datasets) == len(input_datasets): return cls.do_fast_split(input_datasets, toc_file_datasets, subdir_generator_function, split_params) return cls.do_slow_split(input_datasets, subdir_generator_function, split_params)
split = classmethod(split)
[docs] def process_split_file(data): """ This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine) to create the input files for the Task. The parameters: data - a dict containing the contents of the split file """ args = data['args'] input_name = data['input_name'] output_name = data['output_name'] start_sequence = long(args['start_sequence']) sequence_count = long(args['num_sequences']) if 'toc_file' in args: toc_file = json.load(open(args['toc_file'], 'r')) commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count) else: commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count) for cmd in commands: subprocess.check_call(cmd, shell=True) return True
process_split_file = staticmethod(process_split_file)
[docs] @staticmethod def sangerQualities(lines): """Presuming lines are lines from a fastq file, return True if the qualities are compatible with sanger encoding""" for line in islice(lines, 3, None, 4): if not all(_ >= '!' and _ <= 'M' for _ in line[0]): return False return True
[docs]class Fastq(BaseFastq): """Class representing a generic FASTQ sequence""" edam_format = "format_1930" file_ext = "fastq"
[docs]class FastqSanger(Fastq): """Class representing a FASTQ sequence ( the Sanger variant )""" edam_format = "format_1932" file_ext = "fastqsanger"
[docs]class FastqSolexa(Fastq): """Class representing a FASTQ sequence ( the Solexa variant )""" edam_format = "format_1933" file_ext = "fastqsolexa"
[docs]class FastqIllumina(Fastq): """Class representing a FASTQ sequence ( the Illumina 1.3+ variant )""" edam_format = "format_1931" file_ext = "fastqillumina"
[docs]class FastqCSSanger(Fastq): """Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )""" file_ext = "fastqcssanger"
[docs]class FastqGz (BaseFastq, Binary): """Class representing a generic compressed FASTQ sequence""" edam_format = "format_1930" file_ext = "fastq.gz" compressed = True
[docs] def sniff(self, filename): """Determines whether the file is in gzip-compressed FASTQ format""" if not is_gzip(filename): return False return BaseFastq.sniff(self, filename)
[docs]class FastqSangerGz(FastqGz): """Class representing a compressed FASTQ sequence ( the Sanger variant )""" edam_format = "format_1932" file_ext = "fastqsanger.gz"
[docs]class FastqSolexaGz(FastqGz): """Class representing a compressed FASTQ sequence ( the Solexa variant )""" edam_format = "format_1933" file_ext = "fastqsolexa.gz"
if SNIFF_COMPRESSED_FASTQS: Binary.register_sniffable_binary_format("fastqsanger.gz", "fastqsanger.gz", FastqSangerGz) Binary.register_sniffable_binary_format("fastq.gz", "fastq.gz", FastqGz)
[docs]class FastqIlluminaGz(FastqGz): """Class representing a compressed FASTQ sequence ( the Illumina 1.3+ variant )""" edam_format = "format_1931" file_ext = "fastqillumina.gz"
[docs]class FastqCSSangerGz(FastqGz): """Class representing a Color Space compressed FASTQ sequence ( e.g a SOLiD variant )""" file_ext = "fastqcssanger.gz"
[docs]class FastqBz2 (BaseFastq, Binary): """Class representing a generic compressed FASTQ sequence""" edam_format = "format_1930" file_ext = "fastq.bz2" compressed = True
[docs] def sniff(self, filename): """Determine whether the file is in bzip2-compressed FASTQ format""" if not is_bz2(filename): return False return BaseFastq.sniff(self, filename)
[docs]class FastqSangerBz2(FastqBz2): """Class representing a compressed FASTQ sequence ( the Sanger variant )""" edam_format = "format_1932" file_ext = "fastqsanger.bz2"
if SNIFF_COMPRESSED_FASTQS: Binary.register_sniffable_binary_format("fastqsanger.bz2", "fastqsanger.bz2", FastqSangerBz2) Binary.register_sniffable_binary_format("fastq.bz2", "fastq.bz2", FastqBz2)
[docs]class FastqSolexaBz2(FastqBz2): """Class representing a compressed FASTQ sequence ( the Solexa variant )""" edam_format = "format_1933" file_ext = "fastqsolexa.bz2"
[docs]class FastqIlluminaBz2(FastqBz2): """Class representing a compressed FASTQ sequence ( the Illumina 1.3+ variant )""" edam_format = "format_1931" file_ext = "fastqillumina.bz2"
[docs]class FastqCSSangerBz2(FastqBz2): """Class representing a Color Space compressed FASTQ sequence ( e.g a SOLiD variant )""" file_ext = "fastqcssanger.bz2"
[docs]class Maf(Alignment): """Class describing a Maf alignment""" edam_format = "format_3008" file_ext = "maf" # Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition MetadataElement(name="blocks", default=0, desc="Number of blocks", readonly=True, optional=True, visible=False, no_value=0) MetadataElement(name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True) MetadataElement(name="maf_index", desc="MAF Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True)
[docs] def init_meta(self, dataset, copy_from=None): Alignment.init_meta(self, dataset, copy_from=copy_from)
[docs] def set_meta(self, dataset, overwrite=True, **kwd): """ Parses and sets species, chromosomes, index from MAF file. """ # these metadata values are not accessable by users, always overwrite # Imported here to avoid circular dependency from galaxy.tools.util.maf_utilities import build_maf_index_species_chromosomes indexes, species, species_chromosomes, blocks = build_maf_index_species_chromosomes(dataset.file_name) if indexes is None: return # this is not a MAF file dataset.metadata.species = species dataset.metadata.blocks = blocks # write species chromosomes to a file chrom_file = dataset.metadata.species_chromosomes if not chrom_file: chrom_file = dataset.metadata.spec['species_chromosomes'].param.new_file(dataset=dataset) chrom_out = open(chrom_file.file_name, 'wb') for spec, chroms in species_chromosomes.items(): chrom_out.write("%s\t%s\n" % (spec, "\t".join(chroms))) chrom_out.close() dataset.metadata.species_chromosomes = chrom_file index_file = dataset.metadata.maf_index if not index_file: index_file = dataset.metadata.spec['maf_index'].param.new_file(dataset=dataset) indexes.write(open(index_file.file_name, 'wb')) dataset.metadata.maf_index = index_file
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method dataset.peek = data.get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) if dataset.metadata.blocks: dataset.blurb = "%s blocks" % util.commaify(str(dataset.metadata.blocks)) else: # Number of blocks is not known ( this should not happen ), and auto-detect is # needed to set metadata dataset.blurb = "? blocks" else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def display_peek(self, dataset): """Returns formated html of peek""" return self.make_html_table(dataset)
[docs] def make_html_table(self, dataset, skipchars=[]): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] try: out.append('<tr><th>Species:&nbsp;') for species in dataset.metadata.species: out.append('%s&nbsp;' % species) out.append('</th></tr>') if not dataset.peek: dataset.set_peek() data = dataset.peek lines = data.splitlines() for line in lines: line = line.strip() if not line: continue out.append('<tr><td>%s</td></tr>' % escape(line)) out.append('</table>') out = "".join(out) except Exception as exc: out = "Can't create peek %s" % exc return out
[docs] def sniff(self, filename): """ Determines wether the file is in maf format The .maf format is line-oriented. Each multiple alignment ends with a blank line. Each sequence in an alignment is on a single line, which can get quite long, but there is no length limit. Words in a line are delimited by any white space. Lines starting with # are considered to be comments. Lines starting with ## can be ignored by most programs, but contain meta-data of one form or another. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated variable=value pairs. There should be no white space surrounding the "=". For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format5 >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'sequence.maf' ) >>> Maf().sniff( fname ) True >>> fname = get_test_fname( 'sequence.fasta' ) >>> Maf().sniff( fname ) False """ headers = get_headers(filename, None) try: if len(headers) > 1 and headers[0][0] and headers[0][0] == "##maf": return True else: return False except: return False
[docs]class MafCustomTrack(data.Text): file_ext = "mafcustomtrack" MetadataElement(name="vp_chromosome", default='chr1', desc="Viewport Chromosome", readonly=True, optional=True, visible=False, no_value='') MetadataElement(name="vp_start", default='1', desc="Viewport Start", readonly=True, optional=True, visible=False, no_value='') MetadataElement(name="vp_end", default='100', desc="Viewport End", readonly=True, optional=True, visible=False, no_value='')
[docs] def set_meta(self, dataset, overwrite=True, **kwd): """ Parses and sets viewport metadata from MAF file. """ max_block_check = 10 chrom = None forward_strand_start = float('inf') forward_strand_end = 0 try: maf_file = open(dataset.file_name) maf_file.readline() # move past track line for i, block in enumerate(bx.align.maf.Reader(maf_file)): ref_comp = block.get_component_by_src_start(dataset.metadata.dbkey) if ref_comp: ref_chrom = bx.align.maf.src_split(ref_comp.src)[-1] if chrom is None: chrom = ref_chrom if chrom == ref_chrom: forward_strand_start = min(forward_strand_start, ref_comp.forward_strand_start) forward_strand_end = max(forward_strand_end, ref_comp.forward_strand_end) if i > max_block_check: break if forward_strand_end > forward_strand_start: dataset.metadata.vp_chromosome = chrom dataset.metadata.vp_start = forward_strand_start dataset.metadata.vp_end = forward_strand_end except: pass
[docs]class Axt(data.Text): """Class describing an axt alignment""" # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. edam_data = "data_0863" edam_format = "format_3013" file_ext = "axt"
[docs] def sniff(self, filename): """ Determines whether the file is in axt format axt alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields. The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly (line 3) with inserts. Repeats are indicated by lower-case letters. For complete details see http://genome.ucsc.edu/goldenPath/help/axt.html >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'alignment.axt' ) >>> Axt().sniff( fname ) True >>> fname = get_test_fname( 'alignment.lav' ) >>> Axt().sniff( fname ) False """ headers = get_headers(filename, None) if len(headers) < 4: return False for hdr in headers: if len(hdr) > 0 and hdr[0].startswith("##matrix=axt"): return True if len(hdr) > 0 and not hdr[0].startswith("#"): if len(hdr) != 9: return False try: map(int, [hdr[0], hdr[2], hdr[3], hdr[5], hdr[6], hdr[8]]) except: return False if hdr[7] not in data.valid_strand: return False else: return True
[docs]class Lav(data.Text): """Class describing a LAV alignment""" # gvk- 11/19/09 - This is really an alignment, but we no longer have tools that use this data type, and it is # here simply for backward compatibility ( although it is still in the datatypes registry ). Subclassing # from data.Text eliminates managing metadata elements inherited from the Alignemnt class. edam_data = "data_0863" edam_format = "format_3014" file_ext = "lav"
[docs] def sniff(self, filename): """ Determines whether the file is in lav format LAV is an alignment format developed by Webb Miller's group. It is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav. For complete details see http://www.bioperl.org/wiki/LAV_alignment_format >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname( 'alignment.lav' ) >>> Lav().sniff( fname ) True >>> fname = get_test_fname( 'alignment.axt' ) >>> Lav().sniff( fname ) False """ headers = get_headers(filename, None) try: if len(headers) > 1 and headers[0][0] and headers[0][0].startswith('#:lav'): return True else: return False except: return False
[docs]class RNADotPlotMatrix(data.Data): edam_format = "format_3466" file_ext = "rna_eps"
[docs] def set_peek(self, dataset, is_multi_byte=False): if not dataset.dataset.purged: dataset.peek = 'RNA Dot Plot format (Postscript derivative)' dataset.blurb = nice_size(dataset.get_size()) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk'
[docs] def sniff(self, filename): """Determine if the file is in RNA dot plot format.""" if check_image_type(filename, ['EPS']): seq = False coor = False pairs = False with open(filename) as handle: for line in handle: line = line.strip() if line: if line.startswith('/sequence'): seq = True elif line.startswith('/coor'): coor = True elif line.startswith('/pairs'): pairs = True if seq and coor and pairs: return True return False
[docs]class DotBracket (Sequence): edam_data = "data_0880" edam_format = "format_1457" file_ext = "dbn" sequence_regexp = re.compile("^[ACGTURYKMSWBDHVN]+$", re.I) structure_regexp = re.compile("^[\(\)\.\[\]{}]+$")
[docs] def set_meta(self, dataset, **kwd): """ Set the number of sequences and the number of data lines in dataset. """ if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: dataset.metadata.data_lines = None dataset.metadata.sequences = None dataset.metadata.seconday_structures = None return data_lines = 0 sequences = 0 for line in open(dataset.file_name): line = line.strip() data_lines += 1 if line and line.startswith('>'): sequences += 1 dataset.metadata.data_lines = data_lines dataset.metadata.sequences = sequences
[docs] def sniff(self, filename): """ Galaxy Dbn (Dot-Bracket notation) rules: * The first non-empty line is a header line: no comment lines are allowed. * A header line starts with a '>' symbol and continues with 0 or multiple symbols until the line ends. * The second non-empty line is a sequence line. * A sequence line may only include chars that match the FASTA format (https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation) symbols for nucleotides: ACGTURYKMSWBDHVN, and may thus not include whitespaces. * A sequence line has no prefix and no suffix. * A sequence line is case insensitive. * The third non-empty line is a structure (Dot-Bracket) line and only describes the 2D structure of the sequence above it. * A structure line must consist of the following chars: '.{}[]()'. * A structure line must be of the same length as the sequence line, and each char represents the structure of the nucleotide above it. * A structure line has no prefix and no suffix. * A nucleotide pairs with only 1 or 0 other nucleotides. * In a structure line, the number of '(' symbols equals the number of ')' symbols, the number of '[' symbols equals the number of ']' symbols and the number of '{' symbols equals the number of '}' symbols. * The format accepts multiple entries per file, given that each entry is provided as three lines: the header, sequence and structure line. * Sniffing is only applied on the first entry. * Empty lines are allowed. """ state = 0 with open(filename, "r") as handle: for line in handle: line = line.strip() if line: # header line if state == 0: if(line[0] != '>'): return False else: state = 1 # sequence line elif state == 1: if not self.sequence_regexp.match(line): return False else: sequence_size = len(line) state = 2 # dot-bracket structure line elif state == 2: if sequence_size != len(line) or not self.structure_regexp.match(line) or \ line.count('(') != line.count(')') or \ line.count('[') != line.count(']') or \ line.count('{') != line.count('}'): return False else: return True # Number of lines is less than 3 return False
[docs]class Genbank(data.Text): """Class representing a Genbank sequence""" edam_format = "format_1936" edam_data = "data_0849" file_ext = "genbank"
[docs] def sniff(self, filename): try: with open(filename, 'r') as handle: return 'LOCUS ' == handle.read(6) except: pass return False
[docs]class MemePsp(Sequence): """Class representing MEME Position Specific Priors""" file_ext = "memepsp"
[docs] def sniff(self, filename): """ The format of an entry in a PSP file is: >ID WIDTH PRIORS For complete details see http://meme-suite.org/doc/psp-format.html >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('1.memepsp') >>> MemePsp().sniff(fname) True >>> fname = get_test_fname('sequence.fasta') >>> MemePsp().sniff(fname) False """ def floats_verified(l): for item in l.split(): try: float(item) except: return False return True try: num_lines = 0 with open(filename) as fh: line = fh.readline() if not line: # EOF. return False num_lines += 1 if num_lines > 100: return True line = line.strip() if line: if line.startswith('>'): # The line must not be blank, nor start with '>' line = fh.readline().strip() if line == '' or line.startswith('>'): return False # All items within the line must be floats. if not floats_verified(line): return False # If there is a second line within the ID section, # all items within the line must be floats. line = fh.readline().strip() if line: if not floats_verified(line): return False else: # We found a non-empty line, # but it's not a psp id width. return False except: return False # We've reached EOF in less than 100 lines. return True