import stat
import subprocess
import sys
+import tarfile
import time
try:
from htsworkflow.util.alphanum import alphanum
from htsworkflow.util.ethelp import indent, flatten
+from htsworkflow.util.queuecommands import QueueCommands
+
+from htsworkflow.pipelines import srf
class PipelineRun(object):
"""
eland_result = gerald.eland_results.results[end][lane_id]
report.append("Sample name %s" % (eland_result.sample_name))
report.append("Lane id %s end %s" % (eland_result.lane_id, end))
- cluster = summary_results[end][eland_result.lane_id].cluster
- report.append("Clusters %d +/- %d" % (cluster[0], cluster[1]))
+ if end < len(summary_results) and summary_results[end].has_key(eland_result.lane_id):
+ cluster = summary_results[end][eland_result.lane_id].cluster
+ report.append("Clusters %d +/- %d" % (cluster[0], cluster[1]))
report.append("Total Reads: %d" % (eland_result.reads))
if hasattr(eland_result, 'match_codes'):
else:
return False
-def extract_results(runs, output_base_dir=None):
+def save_flowcell_reports(data_dir, cycle_dir):
+ """
+ Save the flowcell quality reports
+ """
+ data_dir = os.path.abspath(data_dir)
+ status_file = os.path.join(data_dir, 'Status.xml')
+ reports_dir = os.path.join(data_dir, 'reports')
+ reports_dest = os.path.join(cycle_dir, 'flowcell-reports.tar.bz2')
+ if os.path.exists(reports_dir):
+ cmd_list = [ 'tar', 'cjvf', reports_dest, 'reports/' ]
+ if os.path.exists(status_file):
+ cmd_list.extend(['Status.xml', 'Status.xsl'])
+ logging.info("Saving reports from " + reports_dir)
+ cwd = os.getcwd()
+ os.chdir(data_dir)
+ q = QueueCommands([" ".join(cmd_list)])
+ q.run()
+ os.chdir(cwd)
+
+
+def save_summary_file(gerald_object, cycle_dir):
+ # Copy Summary.htm
+ summary_path = os.path.join(gerald_object.pathname, 'Summary.htm')
+ if os.path.exists(summary_path):
+ logging.info('Copying %s to %s' % (summary_path, cycle_dir))
+ shutil.copy(summary_path, cycle_dir)
+ else:
+ logging.info('Summary file %s was not found' % (summary_path,))
+
+def save_ivc_plot(bustard_object, cycle_dir):
+ """
+ Save the IVC page and its supporting images
+ """
+ plot_html = os.path.join(bustard_object.pathname, 'IVC.htm')
+ plot_image_path = os.path.join(bustard_object.pathname, 'Plots')
+ plot_images = os.path.join(plot_image_path, 's_?_[a-z]*.png')
+
+ plot_target_path = os.path.join(cycle_dir, 'Plots')
+
+ if os.path.exists(plot_html):
+ logging.debug("Saving %s" % ( plot_html, ))
+ logging.debug("Saving %s" % ( plot_images, ))
+ shutil.copy(plot_html, cycle_dir)
+ if not os.path.exists(plot_target_path):
+ os.mkdir(plot_target_path)
+ for plot_file in glob(plot_images):
+ shutil.copy(plot_file, plot_target_path)
+ else:
+ logging.warning('Missing IVC.html file, not archiving')
+
+
+def compress_score_files(bustard_object, cycle_dir):
+ """
+ Compress score files into our result directory
+ """
+ # check for g.pathname/Temp a new feature of 1.1rc1
+ scores_path = bustard_object.pathname
+ scores_path_temp = os.path.join(scores_path, 'Temp')
+ if os.path.isdir(scores_path_temp):
+ scores_path = scores_path_temp
+
+ # hopefully we have a directory that contains s_*_score files
+ score_files = []
+ for f in os.listdir(scores_path):
+ if re.match('.*_score.txt', f):
+ score_files.append(f)
+
+ tar_cmd = ['tar', 'c'] + score_files
+ bzip_cmd = [ 'bzip2', '-9', '-c' ]
+ tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
+ tar_dest = open(tar_dest_name, 'w')
+ logging.info("Compressing score files from %s" % (scores_path,))
+ logging.info("Running tar: " + " ".join(tar_cmd[:10]))
+ logging.info("Running bzip2: " + " ".join(bzip_cmd))
+ logging.info("Writing to %s" %(tar_dest_name,))
+
+ env = {'BZIP': '-9'}
+ tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, env=env,
+ cwd=scores_path)
+ bzip = subprocess.Popen(bzip_cmd, stdin=tar.stdout, stdout=tar_dest)
+ tar.wait()
+
+
+def compress_eland_results(gerald_object, cycle_dir, num_jobs=1):
+ """
+ Compress eland result files into the archive directory
+ """
+ # copy & bzip eland files
+ bz_commands = []
+
+ for lanes_dictionary in gerald_object.eland_results.results:
+ for eland_lane in lanes_dictionary.values():
+ source_name = eland_lane.pathname
+ path, name = os.path.split(eland_lane.pathname)
+ dest_name = os.path.join(cycle_dir, name)
+ logging.info("Saving eland file %s to %s" % \
+ (source_name, dest_name))
+
+ if is_compressed(name):
+ logging.info('Already compressed, Saving to %s' % (dest_name, ))
+ shutil.copy(source_name, dest_name)
+ else:
+ # not compressed
+ dest_name += '.bz2'
+ args = ['bzip2', '-9', '-c', source_name, '>', dest_name ]
+ bz_commands.append(" ".join(args))
+ #logging.info('Running: %s' % ( " ".join(args) ))
+ #bzip_dest = open(dest_name, 'w')
+ #bzip = subprocess.Popen(args, stdout=bzip_dest)
+ #logging.info('Saving to %s' % (dest_name, ))
+ #bzip.wait()
+
+ if len(bz_commands) > 0:
+ q = QueueCommands(bz_commands, num_jobs)
+ q.run()
+
+
+def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
+ """
+ Iterate over runfolders in runs extracting the most useful information.
+ * run parameters (in run-*.xml)
+ * eland_result files
+ * score files
+ * Summary.htm
+ * srf files (raw sequence & qualities)
+ """
if output_base_dir is None:
output_base_dir = os.getcwd()
else:
os.mkdir(cycle_dir)
- # copy stuff out of the main run
- g = r.gerald
-
# save run file
r.save(cycle_dir)
- # Copy Summary.htm
- summary_path = os.path.join(r.gerald.pathname, 'Summary.htm')
- if os.path.exists(summary_path):
- logging.info('Copying %s to %s' % (summary_path, cycle_dir))
- shutil.copy(summary_path, cycle_dir)
- else:
- logging.info('Summary file %s was not found' % (summary_path,))
-
- # tar score files
- score_files = []
-
- # check for g.pathname/Temp a new feature of 1.1rc1
- scores_path = g.pathname
- scores_path_temp = os.path.join(scores_path, 'Temp')
- if os.path.isdir(scores_path_temp):
- scores_path = scores_path_temp
-
- # hopefully we have a directory that contains s_*_score files
- for f in os.listdir(scores_path):
- if re.match('.*_score.txt', f):
- score_files.append(f)
-
- tar_cmd = ['/bin/tar', 'c'] + score_files
- bzip_cmd = [ 'bzip2', '-9', '-c' ]
- tar_dest_name =os.path.join(cycle_dir, 'scores.tar.bz2')
- tar_dest = open(tar_dest_name, 'w')
- logging.info("Compressing score files from %s" % (scores_path,))
- logging.info("Running tar: " + " ".join(tar_cmd[:10]))
- logging.info("Running bzip2: " + " ".join(bzip_cmd))
- logging.info("Writing to %s" %(tar_dest_name))
-
- env = {'BZIP': '-9'}
- tar = subprocess.Popen(tar_cmd, stdout=subprocess.PIPE, shell=False, env=env,
- cwd=scores_path)
- bzip = subprocess.Popen(bzip_cmd, stdin=tar.stdout, stdout=tar_dest)
- tar.wait()
-
- # copy & bzip eland files
- for lanes_dictionary in g.eland_results.results:
- for eland_lane in lanes_dictionary.values():
- source_name = eland_lane.pathname
- path, name = os.path.split(eland_lane.pathname)
- dest_name = os.path.join(cycle_dir, name)
- logging.info("Saving eland file %s to %s" % \
- (source_name, dest_name))
-
- if is_compressed(name):
- logging.info('Already compressed, Saving to %s' % (dest_name, ))
- shutil.copy(source_name, dest_name)
- else:
- # not compressed
- dest_name += '.bz2'
- args = ['bzip2', '-9', '-c', source_name]
- logging.info('Running: %s' % ( " ".join(args) ))
- bzip_dest = open(dest_name, 'w')
- bzip = subprocess.Popen(args, stdout=bzip_dest)
- logging.info('Saving to %s' % (dest_name, ))
- bzip.wait()
+ # save illumina flowcell status report
+ save_flowcell_reports( os.path.join(r.image_analysis.pathname, '..'), cycle_dir )
+
+ # save stuff from bustard
+ # grab IVC plot
+ save_ivc_plot(r.bustard, cycle_dir)
+
+ # build base call saving commands
+ if site is not None:
+ lanes = range(1,9)
+ run_name = srf.pathname_to_run_name(r.pathname)
+ srf_cmds = srf.make_qseq_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir)
+ srf.run_commands(r.bustard.pathname, srf_cmds, num_jobs)
+
+ # save stuff from GERALD
+ # copy stuff out of the main run
+ g = r.gerald
+ # save summary file
+ save_summary_file(g, cycle_dir)
+
+ # compress eland result files
+ compress_eland_results(g, cycle_dir, num_jobs)
+
+ # md5 all the compressed files once we're done
+ md5_commands = srf.make_md5_commands(cycle_dir)
+ srf.run_commands(cycle_dir, md5_commands, num_jobs)
+
def rm_list(files, dry_run=True):
for f in files:
if os.path.exists(f):
projects / htsworkflow.git / blobdiff