#!/usr/bin/env python
from ConfigParser import SafeConfigParser
+import fnmatch
from glob import glob
import json
import logging
+import netrc
from optparse import OptionParser
import os
from pprint import pprint, pformat
import shlex
from StringIO import StringIO
-import time
+import stat
+from subprocess import Popen, PIPE
import sys
+import time
import types
import urllib
import urllib2
import urlparse
-
from htsworkflow.util import api
from htsworkflow.pipelines.sequences import \
create_sequence_table, \
scan_for_sequences
+from htsworkflow.pipelines import qseq2fastq
+from htsworkflow.pipelines import srf2fastq
-def make_submission_name(ininame):
- base = os.path.basename(ininame)
- name, ext = os.path.splitext(base)
- return name + '.tgz'
+def main(cmdline=None):
+ parser = make_parser()
+ opts, args = parser.parse_args(cmdline)
+
+ if opts.debug:
+ logging.basicConfig(level = logging.DEBUG )
+ elif opts.verbose:
+ logging.basicConfig(level = logging.INFO )
+ else:
+ logging.basicConfig(level = logging.WARNING )
+
+ apidata = {'apiid': opts.apiid, 'apikey': opts.apikey }
-def make_ddf_name(pathname):
- base = os.path.basename(pathname)
- name, ext = os.path.splitext(base)
- return name + '.ddf'
+ if opts.host is None or opts.apiid is None or opts.apikey is None:
+ parser.error("Please specify host url, apiid, apikey")
-def make_condor_name(pathname):
- base = os.path.basename(pathname)
- name, ext = os.path.splitext(base)
- return name + '.condor'
+ if opts.makeddf and opts.daf is None:
+ parser.error("Please specify your daf when making ddf files")
+
+ if len(args) == 0:
+ parser.error("I need at least one library submission-dir input file")
+
+ library_result_map = []
+ for a in args:
+ library_result_map.extend(read_library_result_map(a))
+
+ if opts.make_tree_from is not None:
+ make_tree_from(opts.make_tree_from, library_result_map)
+
+ if opts.daf is not None:
+ link_daf(opts.daf, library_result_map)
+
+ if opts.fastq:
+ build_fastqs(opts.host,
+ apidata,
+ opts.sequence,
+ library_result_map,
+ force=opts.force)
+
+ if opts.ini:
+ make_submission_ini(opts.host, apidata, library_result_map)
+
+ if opts.makeddf:
+ make_all_ddfs(library_result_map, opts.daf, force=opts.force)
+
+
+def make_parser():
+ # Load defaults from the config files
+ config = SafeConfigParser()
+ config.read([os.path.expanduser('~/.htsworkflow.ini'), '/etc/htsworkflow.ini'])
-def make_submit_script(target, header, body_list):
- """
- write out a text file
+ sequence_archive = None
+ apiid = None
+ apikey = None
+ apihost = None
+ SECTION = 'sequence_archive'
+ if config.has_section(SECTION):
+ sequence_archive = config.get(SECTION, 'sequence_archive',sequence_archive)
+ sequence_archive = os.path.expanduser(sequence_archive)
+ apiid = config.get(SECTION, 'apiid', apiid)
+ apikey = config.get(SECTION, 'apikey', apikey)
+ apihost = config.get(SECTION, 'host', apihost)
- this was intended for condor submit scripts
+ parser = OptionParser()
+
+ # commands
+ parser.add_option('--make-tree-from',
+ help="create directories & link data files",
+ default=None)
+ parser.add_option('--fastq', help="generate scripts for making fastq files",
+ default=False, action="store_true")
+
+ parser.add_option('--ini', help="generate submission ini file", default=False,
+ action="store_true")
+
+ parser.add_option('--makeddf', help='make the ddfs', default=False,
+ action="store_true")
+
+ parser.add_option('--daf', default=None, help='specify daf name')
+ parser.add_option('--force', default=False, action="store_true",
+ help="Force regenerating fastqs")
+
+ # configuration options
+ parser.add_option('--apiid', default=apiid, help="Specify API ID")
+ parser.add_option('--apikey', default=apikey, help="Specify API KEY")
+ parser.add_option('--host', default=apihost,
+ help="specify HTSWorkflow host",)
+ parser.add_option('--sequence', default=sequence_archive,
+ help="sequence repository")
+
+ # debugging
+ parser.add_option('--verbose', default=False, action="store_true",
+ help='verbose logging')
+ parser.add_option('--debug', default=False, action="store_true",
+ help='debug logging')
+
+ return parser
+
+
+def make_tree_from(source_path, library_result_map):
+ """Create a tree using data files from source path.
+ """
+ for lib_id, lib_path in library_result_map:
+ if not os.path.exists(lib_path):
+ logging.info("Making dir {0}".format(lib_path))
+ os.mkdir(lib_path)
+ source_lib_dir = os.path.join(source_path, lib_path)
+ if os.path.exists(source_lib_dir):
+ pass
+ for filename in os.listdir(source_lib_dir):
+ source_pathname = os.path.join(source_lib_dir, filename)
+ target_pathname = os.path.join(lib_path, filename)
+ if not os.path.exists(source_pathname):
+ raise IOError("{0} does not exist".format(source_pathname))
+ if not os.path.exists(target_pathname):
+ os.symlink(source_pathname, target_pathname)
+ logging.info(
+ 'LINK {0} to {1}'.format(source_pathname, target_pathname))
+
+def build_fastqs(host, apidata, sequences_path, library_result_map,
+ force=False ):
+ """
+ Generate condor scripts to build any needed fastq files
Args:
- target (str or stream):
- if target is a string, we will open and close the file
- if target is a stream, the caller is responsible.
+ host (str): root of the htsworkflow api server
+ apidata (dict): id & key to post to the server
+ sequences_path (str): root of the directory tree to scan for files
+ library_result_map (list): [(library_id, destination directory), ...]
+ """
+ qseq_condor_header = """
+Universe=vanilla
+executable=%(exe)s
+error=log/qseq2fastq.err.$(process).log
+output=log/qseq2fastq.out.$(process).log
+log=log/qseq2fastq.log
- header (str);
- header to write at the beginning of the file
- body_list (list of strs):
- a list of blocks to add to the file.
+""" % {'exe': sys.executable }
+ qseq_condor_entries = []
+ srf_condor_header = """
+Universe=vanilla
+executable=%(exe)s
+output=log/srf_pair_fastq.out.$(process).log
+error=log/srf_pair_fastq.err.$(process).log
+log=log/srf_pair_fastq.log
+environment="PYTHONPATH=/home/diane/lib/python2.6/site-packages:/home/diane/proj/solexa/gaworkflow PATH=/woldlab/rattus/lvol0/mus/home/diane/bin:/usr/bin:/bin"
+
+""" % {'exe': sys.executable }
+ srf_condor_entries = []
+ lib_db = find_archive_sequence_files(host,
+ apidata,
+ sequences_path,
+ library_result_map)
+
+ needed_targets = find_missing_targets(library_result_map, lib_db, force)
+
+ for target_pathname, available_sources in needed_targets.items():
+ logging.debug(' target : %s' % (target_pathname,))
+ logging.debug(' candidate sources: %s' % (available_sources,))
+ if available_sources.has_key('qseq'):
+ source = available_sources['qseq']
+ qseq_condor_entries.append(
+ condor_qseq_to_fastq(source.path,
+ target_pathname,
+ source.flowcell,
+ force=force)
+ )
+ elif available_sources.has_key('srf'):
+ source = available_sources['srf']
+ mid = getattr(source, 'mid_point', None)
+ srf_condor_entries.append(
+ condor_srf_to_fastq(source.path,
+ target_pathname,
+ source.paired,
+ source.flowcell,
+ mid,
+ force=force)
+ )
+ else:
+ print " need file", target_pathname
+
+ if len(srf_condor_entries) > 0:
+ make_submit_script('srf.fastq.condor',
+ srf_condor_header,
+ srf_condor_entries)
+
+ if len(qseq_condor_entries) > 0:
+ make_submit_script('qseq.fastq.condor',
+ qseq_condor_header,
+ qseq_condor_entries)
+
+
+def find_missing_targets(library_result_map, lib_db, force=False):
"""
- if type(target) in types.StringTypes:
- f = open(target,'w')
- else:
- f = target
- f.write(header)
- for entry in body_list:
- f.write(entry)
- if type(target) in types.StringTypes:
- f.close()
+ Check if the sequence file exists.
+ This requires computing what the sequence name is and checking
+ to see if it can be found in the sequence location.
-def parse_filelist(file_string):
- return file_string.split(',')
+ Adds seq.paired flag to sequences listed in lib_db[*]['lanes']
+ """
+ fastq_paired_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s_r%(read)s.fastq'
+ fastq_single_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s.fastq'
+ # find what targets we're missing
+ needed_targets = {}
+ for lib_id, result_dir in library_result_map:
+ lib = lib_db[lib_id]
+ lane_dict = make_lane_dict(lib_db, lib_id)
+
+ for lane_key, sequences in lib['lanes'].items():
+ for seq in sequences:
+ seq.paired = lane_dict[seq.flowcell]['paired_end']
+ lane_status = lane_dict[seq.flowcell]['status']
-def validate_filelist(files):
+ if seq.paired and seq.read is None:
+ seq.read = 1
+ filename_attributes = {
+ 'flowcell': seq.flowcell,
+ 'lib_id': lib_id,
+ 'lane': seq.lane,
+ 'read': seq.read,
+ 'cycle': seq.cycle
+ }
+ # skip bad runs
+ if lane_status == 'Failed':
+ continue
+ if seq.flowcell == '30DY0AAXX':
+ # 30DY0 only ran for 151 bases instead of 152
+ # it is actually 76 1st read, 75 2nd read
+ seq.mid_point = 76
+
+ # end filters
+ if seq.paired:
+ target_name = fastq_paired_template % filename_attributes
+ else:
+ target_name = fastq_single_template % filename_attributes
+
+ target_pathname = os.path.join(result_dir, target_name)
+ if force or not os.path.exists(target_pathname):
+ t = needed_targets.setdefault(target_pathname, {})
+ t[seq.filetype] = seq
+
+ return needed_targets
+
+
+def link_daf(daf_path, library_result_map):
+ if not os.path.exists(daf_path):
+ raise RuntimeError("%s does not exist, how can I link to it?" % (daf_path,))
+
+ base_daf = os.path.basename(daf_path)
+
+ for lib_id, result_dir in library_result_map:
+ if not os.path.exists(result_dir):
+ raise RuntimeError("Couldn't find target directory %s" %(result_dir,))
+ submission_daf = os.path.join(result_dir, base_daf)
+ if not os.path.exists(submission_daf):
+ if not os.path.exists(daf_path):
+ raise RuntimeError("Couldn't find daf: %s" %(daf_path,))
+ os.link(daf_path, submission_daf)
+
+
+def make_submission_ini(host, apidata, library_result_map, paired=True):
+ #attributes = get_filename_attribute_map(paired)
+ view_map = NameToViewMap(host, apidata)
+
+ candidate_fastq_src = {}
+
+ for lib_id, result_dir in library_result_map:
+ order_by = ['order_by=files', 'view', 'replicate', 'cell',
+ 'readType', 'mapAlgorithm', 'insertLength', 'md5sum' ]
+ inifile = ['[config]']
+ inifile += [" ".join(order_by)]
+ inifile += ['']
+ line_counter = 1
+ result_ini = os.path.join(result_dir, result_dir+'.ini')
+
+ # write other lines
+ submission_files = os.listdir(result_dir)
+ fastqs = {}
+ fastq_attributes = {}
+ for f in submission_files:
+ attributes = view_map.find_attributes(f, lib_id)
+ if attributes is None:
+ raise ValueError("Unrecognized file: %s" % (f,))
+ attributes['md5sum'] = "None"
+
+ ext = attributes["extension"]
+ if attributes['view'] is None:
+ continue
+ elif attributes.get("type", None) == 'fastq':
+ fastqs.setdefault(ext, set()).add(f)
+ fastq_attributes[ext] = attributes
+ else:
+ md5sum = make_md5sum(os.path.join(result_dir,f))
+ if md5sum is not None:
+ attributes['md5sum']=md5sum
+ inifile.extend(
+ make_submission_section(line_counter,
+ [f],
+ attributes
+ )
+ )
+ inifile += ['']
+ line_counter += 1
+ # add in fastqs on a single line.
+
+ for extension, fastq_files in fastqs.items():
+ inifile.extend(
+ make_submission_section(line_counter,
+ fastq_files,
+ fastq_attributes[extension])
+ )
+ inifile += ['']
+ line_counter += 1
+
+ f = open(result_ini,'w')
+ f.write(os.linesep.join(inifile))
+
+
+def make_lane_dict(lib_db, lib_id):
"""
- Die if a file doesn't exist in a file list
+ Convert the lane_set in a lib_db to a dictionary
+ indexed by flowcell ID
"""
- for f in files:
- if not os.path.exists(f):
- raise RuntimeError("%s does not exist" % (f,))
+ result = []
+ for lane in lib_db[lib_id]['lane_set']:
+ result.append((lane['flowcell'], lane))
+ return dict(result)
+
+
+def make_all_ddfs(library_result_map, daf_name, make_condor=True, force=False):
+ dag_fragment = []
+ for lib_id, result_dir in library_result_map:
+ ininame = result_dir+'.ini'
+ inipathname = os.path.join(result_dir, ininame)
+ if os.path.exists(inipathname):
+ dag_fragment.extend(
+ make_ddf(ininame, daf_name, True, make_condor, result_dir)
+ )
+
+ if make_condor and len(dag_fragment) > 0:
+ dag_filename = 'submission.dagman'
+ if not force and os.path.exists(dag_filename):
+ logging.warn("%s exists, please delete" % (dag_filename,))
+ else:
+ f = open(dag_filename,'w')
+ f.write( os.linesep.join(dag_fragment))
+ f.write( os.linesep )
+ f.close()
+
+
+def make_ddf(ininame, daf_name, guess_ddf=False, make_condor=False, outdir=None):
+ """
+ Make ddf files, and bonus condor file
+ """
+ dag_fragments = []
+ curdir = os.getcwd()
+ if outdir is not None:
+ os.chdir(outdir)
+ output = sys.stdout
+ ddf_name = None
+ if guess_ddf:
+ ddf_name = make_ddf_name(ininame)
+ print ddf_name
+ output = open(ddf_name,'w')
+
+ file_list = read_ddf_ini(ininame, output)
+ logging.info(
+ "Read config {0}, found files: {1}".format(
+ ininame, ", ".join(file_list)))
+
+ file_list.append(daf_name)
+ if ddf_name is not None:
+ file_list.append(ddf_name)
+
+ if make_condor:
+ archive_condor = make_condor_archive_script(ininame, file_list)
+ upload_condor = make_condor_upload_script(ininame)
+
+ dag_fragments.extend(
+ make_dag_fragment(ininame, archive_condor, upload_condor)
+ )
+
+ os.chdir(curdir)
+
+ return dag_fragments
+
def read_ddf_ini(filename, output=sys.stdout):
"""
output.write("\t".join(values))
output.write(os.linesep)
return file_list
-
+
+
+def read_library_result_map(filename):
+ """
+ Read a file that maps library id to result directory.
+ Does not support spaces in filenames.
+
+ For example:
+ 10000 result/foo/bar
+ """
+ stream = open(filename,'r')
+
+ results = []
+ for line in stream:
+ line = line.rstrip()
+ if not line.startswith('#') and len(line) > 0 :
+ library_id, result_dir = line.split()
+ results.append((library_id, result_dir))
+ return results
+
+
def make_condor_archive_script(ininame, files):
script = """Universe = vanilla
Executable = /bin/tar
-arguments = czvf ../%(archivename)s %(filelist)s
+arguments = czvhf ../%(archivename)s %(filelist)s
Error = compress.err.$(Process).log
Output = compress.out.$(Process).log
-Log = compress.log
+Log = /tmp/submission-compress-%(user)s.log
initialdir = %(initialdir)s
+environment="GZIP=-3"
+request_memory = 20
queue
"""
context = {'archivename': make_submission_name(ininame),
'filelist': " ".join(files),
- 'initialdir': os.getcwd()}
+ 'initialdir': os.getcwd(),
+ 'user': os.getlogin()}
- condor_script = make_condor_name(ininame)
+ condor_script = make_condor_name(ininame, 'archive')
condor_stream = open(condor_script,'w')
condor_stream.write(script % context)
condor_stream.close()
+ return condor_script
-def make_ddf(ininame, daf_name, guess_ddf=False, make_condor=False, outdir=None):
- """
- Make ddf files, and bonus condor file
- """
- curdir = os.getcwd()
- if outdir is not None:
- os.chdir(outdir)
- output = sys.stdout
- ddf_name = None
- if guess_ddf:
- ddf_name = make_ddf_name(ininame)
- print ddf_name
- output = open(ddf_name,'w')
- file_list = read_ddf_ini(ininame, output)
+def make_condor_upload_script(ininame):
+ script = """Universe = vanilla
+
+Executable = /usr/bin/lftp
+arguments = -c put ../%(archivename)s -o ftp://%(ftpuser)s:%(ftppassword)s@%(ftphost)s/%(archivename)s
+
+Error = upload.err.$(Process).log
+Output = upload.out.$(Process).log
+Log = /tmp/submission-upload-%(user)s.log
+initialdir = %(initialdir)s
+
+queue
+"""
+ auth = netrc.netrc(os.path.expanduser("~diane/.netrc"))
+
+ encodeftp = 'encodeftp.cse.ucsc.edu'
+ ftpuser = auth.hosts[encodeftp][0]
+ ftppassword = auth.hosts[encodeftp][2]
+ context = {'archivename': make_submission_name(ininame),
+ 'initialdir': os.getcwd(),
+ 'user': os.getlogin(),
+ 'ftpuser': ftpuser,
+ 'ftppassword': ftppassword,
+ 'ftphost': encodeftp}
+
+ condor_script = make_condor_name(ininame, 'upload')
+ condor_stream = open(condor_script,'w')
+ condor_stream.write(script % context)
+ condor_stream.close()
+ os.chmod(condor_script, stat.S_IREAD|stat.S_IWRITE)
+
+ return condor_script
+
+
+def make_dag_fragment(ininame, archive_condor, upload_condor):
+ """
+ Make the couple of fragments compress and then upload the data.
+ """
+ cur_dir = os.getcwd()
+ archive_condor = os.path.join(cur_dir, archive_condor)
+ upload_condor = os.path.join(cur_dir, upload_condor)
+ job_basename = make_base_name(ininame)
- file_list.append(daf_name)
- if ddf_name is not None:
- file_list.append(ddf_name)
+ fragments = []
+ fragments.append('JOB %s_archive %s' % (job_basename, archive_condor))
+ fragments.append('JOB %s_upload %s' % (job_basename, upload_condor))
+ fragments.append('PARENT %s_archive CHILD %s_upload' % (job_basename, job_basename))
- if make_condor:
- make_condor_archive_script(ininame, file_list)
-
- os.chdir(curdir)
+ return fragments
def get_library_info(host, apidata, library_id):
url = api.library_url(host, library_id)
contents = api.retrieve_info(url, apidata)
return contents
-
-def read_library_result_map(filename):
- stream = open(filename,'r')
- results = []
- for line in stream:
- if not line.startswith('#'):
- library_id, result_dir = line.strip().split()
- results.append((library_id, result_dir))
- return results
-def condor_srf_to_fastq(srf_file, target_pathname):
- script = """output=%(target_pathname)s
-arguments="-c %(srf_file)s"
+def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None,
+ mid=None, force=False):
+ py = srf2fastq.__file__
+ args = [ py, srf_file, ]
+ if paired:
+ args.extend(['--left', target_pathname])
+ # this is ugly. I did it because I was pregenerating the target
+ # names before I tried to figure out what sources could generate
+ # those targets, and everything up to this point had been
+ # one-to-one. So I couldn't figure out how to pair the
+ # target names.
+ # With this at least the command will run correctly.
+ # however if we rename the default targets, this'll break
+ # also I think it'll generate it twice.
+ args.extend(['--right',
+ target_pathname.replace('_r1.fastq', '_r2.fastq')])
+ else:
+ args.extend(['--single', target_pathname ])
+ if flowcell is not None:
+ args.extend(['--flowcell', flowcell])
+
+ if mid is not None:
+ args.extend(['-m', str(mid)])
+
+ if force:
+ args.extend(['--force'])
+
+ script = """
+arguments="%s"
queue
-"""
- params = {'srf_file': srf_file,
- 'target_pathname': target_pathname}
+""" % (" ".join(args),)
- return script % params
+ return script
-def condor_qseq_to_fastq(qseq_file, target_pathname):
+
+def condor_qseq_to_fastq(qseq_file, target_pathname, flowcell=None, force=False):
+ py = qseq2fastq.__file__
+ args = [py, '-i', qseq_file, '-o', target_pathname ]
+ if flowcell is not None:
+ args.extend(['-f', flowcell])
script = """
-arguments="-i %(qseq_file)s -o %(target_pathname)s"
+arguments="%s"
queue
-"""
- params = {'qseq_file': qseq_file,
- 'target_pathname': target_pathname}
-
- return script % params
+""" % (" ".join(args))
+
+ return script
def find_archive_sequence_files(host, apidata, sequences_path,
library_result_map):
candidate_lanes = {}
for lib_id, result_dir in library_result_map:
lib_info = get_library_info(host, apidata, lib_id)
+ lib_info['lanes'] = {}
lib_db[lib_id] = lib_info
for lane in lib_info['lane_set']:
lib_id = candidate_lanes.get(lane_key, None)
if lib_id is not None:
lib_info = lib_db[lib_id]
- lanes = lib_info.setdefault('lanes', {})
- lanes.setdefault(lane_key, set()).add(seq)
+ lib_info['lanes'].setdefault(lane_key, set()).add(seq)
return lib_db
-def build_fastqs(host, apidata, sequences_path, library_result_map,
- paired=True ):
- """
- Generate condor scripts to build any needed fastq files
-
- Args:
- host (str): root of the htsworkflow api server
- apidata (dict): id & key to post to the server
- sequences_path (str): root of the directory tree to scan for files
- library_result_map (list): [(library_id, destination directory), ...]
- paired: should we assume that we are processing paired end records?
- if False, we will treat this as single ended.
- """
- qseq_condor_header = """
-Universe=vanilla
-executable=/woldlab/rattus/lvol0/mus/home/diane/proj/gaworkflow/scripts/qseq2fastq
-error=qseqfastq.err.$(process).log
-output=qseqfastq.out.$(process).log
-log=qseqfastq.log
-
-"""
- qseq_condor_entries = []
- srf_condor_header = """
-Universe=vanilla
-executable=/woldlab/rattus/lvol0/mus/home/diane/bin/srf2fastq
-output=srf2fastq.out.$(process).log
-error=srf2fastq.err.$(process).log
-log=srffastq.log
-"""
- srf_condor_entries = []
- fastq_paired_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s_r%(read)s.fastq'
- fastq_single_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s.fastq'
- lib_db = find_archive_sequence_files(host,
- apidata,
- sequences_path,
- library_result_map)
+class NameToViewMap(object):
+ """Determine view attributes for a given submission file name
+ """
+ def __init__(self, root_url, apidata):
+ self.root_url = root_url
+ self.apidata = apidata
+
+ self.lib_cache = {}
+ self.lib_paired = {}
+ # ma is "map algorithm"
+ ma = 'TH1014'
+
+ self.patterns = [
+ ('*.bai', None),
+ ('*.splices.bam', 'Splices'),
+ ('*.bam', self._guess_bam_view),
+ ('junctions.bed', 'Junctions'),
+ ('*.jnct', 'Junctions'),
+ ('*unique.bigwig', None),
+ ('*plus.bigwig', 'PlusSignal'),
+ ('*minus.bigwig', 'MinusSignal'),
+ ('*.bigwig', 'Signal'),
+ ('*.tar.bz2', None),
+ ('*.condor', None),
+ ('*.daf', None),
+ ('*.ddf', None),
+
+ ('*ufflinks?0.9.3.genes.gtf', 'GeneDeNovo'),
+ ('*ufflinks?0.9.3.transcripts.gtf', 'TranscriptDeNovo'),
+ ('*GENCODE-v3c.exonFPKM.gtf', 'ExonsGencV3c'),
+ ('*GENCODE-v3c.genes.gtf', 'GeneGencV3c'),
+ ('*GENCODE-v3c.transcripts.gtf', 'TranscriptGencV3c'),
+ ('*GENCODE-v3c.TSS.gtf', 'TSS'),
+ ('*.junctions.bed6+3', 'Junctions'),
+
+ ('*.?ufflinks-0.9.0?genes.expr', 'GeneDeNovo'),
+ ('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
+ ('*.?ufflinks-0.9.0?transcripts.gtf', 'GeneModel'),
+
+ ('*.GENCODE-v3c?genes.expr', 'GeneGCV3c'),
+ ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
+ ('*.GENCODE-v3c?transcript*.gtf', 'TranscriptGencV3c'),
+ ('*.GENCODE-v4?genes.expr', None), #'GeneGCV4'),
+ ('*.GENCODE-v4?transcript*.expr', None), #'TranscriptGCV4'),
+ ('*.GENCODE-v4?transcript*.gtf', None), #'TranscriptGencV4'),
+ ('*_1.75mers.fastq', 'FastqRd1'),
+ ('*_2.75mers.fastq', 'FastqRd2'),
+ ('*_r1.fastq', 'FastqRd1'),
+ ('*_r2.fastq', 'FastqRd2'),
+ ('*.fastq', 'Fastq'),
+ ('*.gtf', 'GeneModel'),
+ ('*.ini', None),
+ ('*.log', None),
+ ('*.md5', None),
+ ('paired-end-distribution*', 'InsLength'),
+ ('*.stats.txt', 'InsLength'),
+ ('*.srf', None),
+ ('*.wig', None),
+ ('*.zip', None),
+ ('transfer_log', None),
+ ]
+
+ self.views = {
+ None: {"MapAlgorithm": "NA"},
+ "Paired": {"MapAlgorithm": ma},
+ "Aligns": {"MapAlgorithm": ma},
+ "Single": {"MapAlgorithm": ma},
+ "Splices": {"MapAlgorithm": ma},
+ "Junctions": {"MapAlgorithm": ma},
+ "PlusSignal": {"MapAlgorithm": ma},
+ "MinusSignal": {"MapAlgorithm": ma},
+ "Signal": {"MapAlgorithm": ma},
+ "GeneModel": {"MapAlgorithm": ma},
+ "GeneDeNovo": {"MapAlgorithm": ma},
+ "TranscriptDeNovo": {"MapAlgorithm": ma},
+ "ExonsGencV3c": {"MapAlgorithm": ma},
+ "GeneGencV3c": {"MapAlgorithm": ma},
+ "TSS": {"MapAlgorithm": ma},
+ "GeneGCV3c": {"MapAlgorithm": ma},
+ "TranscriptGCV3c": {"MapAlgorithm": ma},
+ "TranscriptGencV3c": {"MapAlgorithm": ma},
+ "GeneGCV4": {"MapAlgorithm": ma},
+ "TranscriptGCV4": {"MapAlgorithm": ma},
+ "FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"},
+ "FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"},
+ "Fastq": {"MapAlgorithm": "NA", "type": "fastq" },
+ "InsLength": {"MapAlgorithm": ma},
+ }
+ # view name is one of the attributes
+ for v in self.views.keys():
+ self.views[v]['view'] = v
+
+ def find_attributes(self, pathname, lib_id):
+ """Looking for the best extension
+ The 'best' is the longest match
+
+ :Args:
+ filename (str): the filename whose extention we are about to examine
+ """
+ path, filename = os.path.splitext(pathname)
+ if not self.lib_cache.has_key(lib_id):
+ self.lib_cache[lib_id] = get_library_info(self.root_url,
+ self.apidata, lib_id)
+
+ lib_info = self.lib_cache[lib_id]
+ if lib_info['cell_line'].lower() == 'unknown':
+ logging.warn("Library %s missing cell_line" % (lib_id,))
+ attributes = {
+ 'cell': lib_info['cell_line'],
+ 'replicate': lib_info['replicate'],
+ }
+ is_paired = self._is_paired(lib_id, lib_info)
+
+ if is_paired:
+ attributes.update(self.get_paired_attributes(lib_info))
+ else:
+ attributes.update(self.get_single_attributes(lib_info))
+
+ for pattern, view in self.patterns:
+ if fnmatch.fnmatch(pathname, pattern):
+ if callable(view):
+ view = view(is_paired=is_paired)
+
+ attributes.update(self.views[view])
+ attributes["extension"] = pattern
+ return attributes
- # find what targets we're missing
- needed_targets = {}
- for lib_id, result_dir in library_result_map:
- lib = lib_db[lib_id]
- for lane_key, sequences in lib['lanes'].items():
- for seq in sequences:
- filename_attributes = {
- 'flowcell': seq.flowcell,
- 'lib_id': lib_id,
- 'lane': seq.lane,
- 'read': seq.read,
- 'cycle': seq.cycle
- }
- # throw out test runs
- # FIXME: this should probably be configurable
- if seq.cycle < 50:
- continue
- if seq.flowcell == '30CUUAAXX':
- # 30CUUAAXX run sucked
- continue
- # end filters
- if paired:
- target_name = fastq_paired_template % filename_attributes
+ def _guess_bam_view(self, is_paired=True):
+ """Guess a view name based on library attributes
+ """
+ if is_paired:
+ return "Paired"
+ else:
+ return "Aligns"
+
+
+ def _is_paired(self, lib_id, lib_info):
+ """Determine if a library is paired end"""
+ if len(lib_info["lane_set"]) == 0:
+ return False
+
+ if not self.lib_paired.has_key(lib_id):
+ is_paired = 0
+ isnot_paired = 0
+ failed = 0
+ # check to see if all the flowcells are the same.
+ # otherwise we might need to do something complicated
+ for flowcell in lib_info["lane_set"]:
+ # yes there's also a status code, but this comparison
+ # is easier to read
+ if flowcell["status"].lower() == "failed":
+ # ignore failed flowcell
+ failed += 1
+ pass
+ elif flowcell["paired_end"]:
+ is_paired += 1
else:
- target_name = fastq_single_template % filename_attributes
-
- target_pathname = os.path.join(result_dir, target_name)
- if not os.path.exists(target_pathname):
- t = needed_targets.setdefault(target_pathname, {})
- t[seq.filetype] = seq
+ isnot_paired += 1
- for target_pathname, available_sources in needed_targets.items():
- logging.debug(' target : %s' % (target_pathname,))
- logging.debug(' candidate sources: %s' % (available_sources,))
- if available_sources.has_key('qseq'):
- source = available_sources['qseq']
- qseq_condor_entries.append(
- condor_qseq_to_fastq(source.path, target_pathname)
- )
- elif available_sources.has_key('srf'):
- source = available_sources['srf']
- if source.read is not None:
- logging.warn(
- "srf -> fastq paired end doesn't work yet: %s" % (source,)
- )
- else:
- srf_condor_entries.append(
- condor_srf_to_fastq(source.path, target_pathname)
- )
- else:
- print " need file", target_pathname
+ logging.debug("Library %s: %d paired, %d single, %d failed" % \
+ (lib_info["library_id"], is_paired, isnot_paired, failed))
- if len(srf_condor_entries) > 0:
- make_submit_script('srf.fastq.condor',
- srf_condor_header,
- srf_condor_entries)
+ if is_paired > isnot_paired:
+ self.lib_paired[lib_id] = True
+ elif is_paired < isnot_paired:
+ self.lib_paired[lib_id] = False
+ else:
+ raise RuntimeError("Equal number of paired & unpaired lanes."\
+ "Can't guess library paired status")
+
+ return self.lib_paired[lib_id]
- if len(qseq_condor_entries) > 0:
- make_submit_script('qseq.fastq.condor',
- qseq_condor_header,
- qseq_condor_entries)
+ def get_paired_attributes(self, lib_info):
+ if lib_info['insert_size'] is None:
+ errmsg = "Library %s is missing insert_size, assuming 200"
+ logging.warn(errmsg % (lib_info["library_id"],))
+ insert_size = 200
+ else:
+ insert_size = lib_info['insert_size']
+ return {'insertLength': insert_size,
+ 'readType': '2x75'}
-def find_best_extension(extension_map, filename):
- """
- Search through extension_map looking for the best extension
- The 'best' is the longest match
+ def get_single_attributes(self, lib_info):
+ return {'insertLength':'ilNA',
+ 'readType': '1x75D'
+ }
- :Args:
- extension_map (dict): '.ext' -> { 'view': 'name' or None }
- filename (str): the filename whose extention we are about to examine
- """
- best_ext = None
- path, last_ext = os.path.splitext(filename)
-
- for ext in extension_map.keys():
- if filename.endswith(ext):
- if best_ext is None:
- best_ext = ext
- elif len(ext) > len(best_ext):
- best_ext = ext
- return best_ext
-
-def make_submission_section(line_counter, files, standard_attributes, file_attributes):
+def make_submission_section(line_counter, files, attributes):
"""
Create a section in the submission ini file
"""
- inifile = [ '[line%s]' % (line_counter,) ]
+ inifile = [ "[line%s]" % (line_counter,) ]
inifile += ["files=%s" % (",".join(files))]
- cur_attributes = {}
- cur_attributes.update(standard_attributes)
- cur_attributes.update(file_attributes)
-
- for k,v in cur_attributes.items():
+
+ for k,v in attributes.items():
inifile += ["%s=%s" % (k,v)]
return inifile
-
-def make_submission_ini(host, apidata, library_result_map):
- attributes = {
- '.bai': {'view': None}, # bam index
- '.bam': {'view': 'Signal'},
- '.splices.bam': {'view': 'Splices'},
- '.bed': {'view': 'TopHatJunctions'},
- '.bigwig': {'view': 'RawSigna'},
- '.tar.bz2': {'view': None},
- '.condor': {'view': None},
- '.daf': {'view': None},
- '.ddf': {'view': None},
- 'novel.genes.expr': {'view': 'GeneDeNovoFPKM'},
- 'novel.transcripts.expr': {'view': 'TranscriptDeNovoFPKM'},
- '.genes.expr': {'view': 'GeneFPKM'},
- '.transcripts.expr': {'view': 'TranscriptFPKM'},
- '.fastq': {'view': 'Fastq' },
- '_r1.fastq': {'view': 'FastqRd1'},
- '_r2.fastq': {'view': 'FastqRd2'},
- '.gtf': {'view': 'CufflinksGeneModel'},
- '.ini': {'view': None},
- '.log': {'view': None},
- '.stats.txt': {'view': 'InsLength'},
- '.srf': {'view': None},
- '.wig': {'view': 'RawSignal'},
- }
-
- candidate_fastq_src = {}
- for lib_id, result_dir in library_result_map:
- inifile = ['[config]']
- inifile += ['order_by=files view cell localization rnaExtract mapAlgorithm readType replicate labVersion']
- inifile += ['']
- line_counter = 1
- lib_info = get_library_info(host, apidata, lib_id)
- result_ini = os.path.join(result_dir, result_dir+'.ini')
-
- if lib_info['cell_line'].lower() == 'unknown':
- logging.warn("Library %s missing cell_line" % (lib_id,))
-
- standard_attributes = {'cell': lib_info['cell_line'],
- 'insertLength': '200',
- 'labVersion': 'TopHat',
- 'localization': 'cell',
- 'mapAlgorithm': 'TopHat',
- 'readType': '2x75',
- 'replicate': lib_info['replicate'],
- 'rnaExtract': 'longPolyA',
- }
-
- # write other lines
- submission_files = os.listdir(result_dir)
- fastqs = {}
- for f in submission_files:
- best_ext = find_best_extension(attributes, f)
-
- if best_ext is not None:
- if attributes[best_ext]['view'] is None:
-
- continue
- elif best_ext.endswith('fastq'):
- fastqs.setdefault(best_ext, set()).add(f)
- else:
- inifile.extend(
- make_submission_section(line_counter,
- [f],
- standard_attributes,
- attributes[best_ext]
- )
- )
- inifile += ['']
- line_counter += 1
- else:
- raise ValueError("Unrecognized file: %s" % (f,))
- # add in fastqs on a single line.
- for extension, fastq_set in fastqs.items():
- inifile.extend(
- make_submission_section(line_counter,
- fastq_set,
- standard_attributes,
- attributes[extension])
- )
- inifile += ['']
- line_counter += 1
-
- f = open(result_ini,'w')
- f.write(os.linesep.join(inifile))
+def make_base_name(pathname):
+ base = os.path.basename(pathname)
+ name, ext = os.path.splitext(base)
+ return name
-def link_daf(daf_path, library_result_map):
- if not os.path.exists(daf_path):
- raise RuntimeError("%s does not exist, how can I link to it?" % (daf_path,))
- base_daf = os.path.basename(daf_path)
-
- for lib_id, result_dir in library_result_map:
- submission_daf = os.path.join(result_dir, base_daf)
- if not os.path.exists(submission_daf):
- os.link(daf_path, submission_daf)
+def make_submission_name(ininame):
+ name = make_base_name(ininame)
+ return name + ".tgz"
-def make_all_ddfs(library_result_map, daf_name):
- for lib_id, result_dir in library_result_map:
- ininame = result_dir+'.ini'
- inipathname = os.path.join(result_dir, ininame)
- if os.path.exists(inipathname):
- make_ddf(ininame, daf_name, True, True, result_dir)
-
-def make_parser():
- # Load defaults from the config files
- config = SafeConfigParser()
- config.read([os.path.expanduser('~/.htsworkflow.ini'), '/etc/htsworkflow.ini'])
-
- sequence_archive = None
- apiid = None
- apikey = None
- apihost = None
- SECTION = 'sequence_archive'
- if config.has_section(SECTION):
- sequence_archive = config.get(SECTION, 'sequence_archive',sequence_archive)
- sequence_archive = os.path.expanduser(sequence_archive)
- apiid = config.get(SECTION, 'apiid', apiid)
- apikey = config.get(SECTION, 'apikey', apikey)
- apihost = config.get(SECTION, 'host', apihost)
- parser = OptionParser()
+def make_ddf_name(pathname):
+ name = make_base_name(pathname)
+ return name + ".ddf"
- # commands
- parser.add_option('--fastq', help="generate scripts for making fastq files",
- default=False, action="store_true")
- parser.add_option('--ini', help="generate submission ini file", default=False,
- action="store_true")
+def make_condor_name(pathname, run_type=None):
+ name = make_base_name(pathname)
+ elements = [name]
+ if run_type is not None:
+ elements.append(run_type)
+ elements.append("condor")
+ return ".".join(elements)
- parser.add_option('--makeddf', help='make the ddfs', default=False,
- action="store_true")
-
- parser.add_option('--daf', default=None, help='specify daf name')
- # configuration options
- parser.add_option('--apiid', default=apiid, help="Specify API ID")
- parser.add_option('--apikey', default=apikey, help="Specify API KEY")
- parser.add_option('--host', default=apihost,
- help="specify HTSWorkflow host",)
- parser.add_option('--sequence', default=sequence_archive,
- help="sequence repository")
- parser.add_option('--single', default=False, action="store_true",
- help="treat the sequences as single ended runs")
+def make_submit_script(target, header, body_list):
+ """
+ write out a text file
- # debugging
- parser.add_option('--verbose', default=False, action="store_true",
- help='verbose logging')
- parser.add_option('--debug', default=False, action="store_true",
- help='debug logging')
+ this was intended for condor submit scripts
- return parser
+ Args:
+ target (str or stream):
+ if target is a string, we will open and close the file
+ if target is a stream, the caller is responsible.
-def main(cmdline=None):
- parser = make_parser()
- opts, args = parser.parse_args(cmdline)
-
- if opts.debug:
- logging.basicConfig(level = logging.DEBUG )
- elif opts.verbose:
- logging.basicConfig(level = logging.INFO )
+ header (str);
+ header to write at the beginning of the file
+ body_list (list of strs):
+ a list of blocks to add to the file.
+ """
+ if type(target) in types.StringTypes:
+ f = open(target,"w")
else:
- logging.basicConfig(level = logging.WARNING )
-
-
- apidata = {'apiid': opts.apiid, 'apikey': opts.apikey }
-
- if opts.host is None or opts.apiid is None or opts.apikey is None:
- parser.error("Please specify host url, apiid, apikey")
+ f = target
+ f.write(header)
+ for entry in body_list:
+ f.write(entry)
+ if type(target) in types.StringTypes:
+ f.close()
- if len(args) == 0:
- parser.error("I need at least one library submission-dir input file")
-
- library_result_map = []
- for a in args:
- library_result_map.extend(read_library_result_map(a))
+def parse_filelist(file_string):
+ return file_string.split(",")
- if opts.daf is not None:
- link_daf(opts.daf, library_result_map)
- if opts.fastq:
- build_fastqs(opts.host,
- apidata,
- opts.sequence,
- library_result_map,
- not opts.single)
+def validate_filelist(files):
+ """
+ Die if a file doesn't exist in a file list
+ """
+ for f in files:
+ if not os.path.exists(f):
+ raise RuntimeError("%s does not exist" % (f,))
- if opts.ini:
- make_submission_ini(opts.host, apidata, library_result_map)
+def make_md5sum(filename):
+ """Quickly find the md5sum of a file
+ """
+ md5_cache = os.path.join(filename+".md5")
+ print md5_cache
+ if os.path.exists(md5_cache):
+ logging.debug("Found md5sum in {0}".format(md5_cache))
+ stream = open(md5_cache,'r')
+ lines = stream.readlines()
+ md5sum = parse_md5sum_line(lines, filename)
+ else:
+ md5sum = make_md5sum_unix(filename, md5_cache)
+ return md5sum
+
+def make_md5sum_unix(filename, md5_cache):
+ cmd = ["md5sum", filename]
+ logging.debug("Running {0}".format(" ".join(cmd)))
+ p = Popen(cmd, stdout=PIPE)
+ stdin, stdout = p.communicate()
+ retcode = p.wait()
+ logging.debug("Finished {0} retcode {1}".format(" ".join(cmd), retcode))
+ if retcode != 0:
+ logging.error("Trouble with md5sum for {0}".format(filename))
+ return None
+ lines = stdin.split(os.linesep)
+ md5sum = parse_md5sum_line(lines, filename)
+ if md5sum is not None:
+ logging.debug("Caching sum in {0}".format(md5_cache))
+ stream = open(md5_cache, "w")
+ stream.write(stdin)
+ stream.close()
+ return md5sum
+
+def parse_md5sum_line(lines, filename):
+ md5sum, md5sum_filename = lines[0].split()
+ if md5sum_filename != filename:
+ errmsg = "MD5sum and I disagre about filename. {0} != {1}"
+ logging.error(errmsg.format(filename, md5sum_filename))
+ return None
+ return md5sum
- if opts.makeddf:
- make_all_ddfs(library_result_map, opts.daf)
-
if __name__ == "__main__":
main()
projects / htsworkflow.git / blobdiff