remove all caltech pipeline specific code

[htsworkflow.git] / scripts / rerun_eland.py

diff --git a/scripts/rerun_eland.py b/scripts/rerun_eland.py
deleted file mode 100644 (file)
index af06cdd..0000000
--- a/scripts/rerun_eland.py
+++ /dev/null
@@ -1,158 +0,0 @@
-#!/usr/bin/env python
-
-import logging
-from optparse import OptionParser
-import os
-import subprocess
-import sys
-
-from htsworkflow.pipelines import gerald
-from htsworkflow.pipelines.eland import extract_eland_sequence
-from htsworkflow.pipelines import runfolder
-
-def make_query_filename(eland_obj, output_dir):
-    query_name = '%s_%s_eland_query.txt' 
-    query_name %= (eland_obj.sample_name, eland_obj.lane_id)
-
-    query_pathname = os.path.join(output_dir, query_name)
-    
-    if os.path.exists(query_pathname):
-        logging.warn("overwriting %s" % (query_pathname,))
-
-    return query_pathname
-
-def make_result_filename(eland_obj, output_dir):
-    result_name = '%s_%s_eland_result.txt' 
-    result_name %= (eland_obj.sample_name, eland_obj.lane_id)
-
-    result_pathname = os.path.join(output_dir, result_name)
-    
-    if os.path.exists(result_pathname):
-        logging.warn("overwriting %s" % (result_pathname,))
-
-    return result_pathname
-
-def extract_sequence(inpathname, query_pathname, length, dry_run=False):
-    logging.info('extracting %d bases' %(length,))
-    logging.info('extracting from %s' %(inpathname,))
-    logging.info('extracting to %s' %(query_pathname,))
-    
-    if not dry_run: 
-        try:
-            instream = open(inpathname, 'r')
-            outstream = open(query_pathname, 'w')
-            extract_eland_sequence(instream, outstream, 0, length)
-        finally:
-            outstream.close()
-            instream.close()
-    
-def run_eland(length, query_name, genome, result_name, multi=False, dry_run=False):
-    cmdline = ['eland_%d' % (length,), query_name, genome, result_name]
-    if multi:
-        cmdline += ['--multi']
-
-    logging.info('running eland: ' + " ".join(cmdline))
-    if not dry_run:
-        return subprocess.Popen(cmdline)
-    else:
-        return None
-
-
-def rerun(gerald_dir, output_dir, length=25, dry_run=False):
-    """
-    look for eland files in gerald_dir and write a subset to output_dir
-    """
-    logging.info("Extracting %d bp from files in %s" % (length, gerald_dir))
-    g = gerald.gerald(gerald_dir)
-
-    # this will only work if we're only missing the last dir in output_dir
-    if not os.path.exists(output_dir):
-        logging.info("Making %s" %(output_dir,))
-        if not dry_run: os.mkdir(output_dir)
-
-    processes = []
-    for lane_id, lane_param in g.lanes.items():
-        eland = g.eland_results[lane_id]
-
-        inpathname = eland.pathname
-        query_pathname = make_query_filename(eland, output_dir)
-        result_pathname = make_result_filename(eland, output_dir)
-
-        extract_sequence(inpathname, query_pathname, length, dry_run=dry_run)
-
-        p = run_eland(length, 
-                      query_pathname, 
-                      lane_param.eland_genome, 
-                      result_pathname, 
-                      dry_run=dry_run)
-        if p is not None:
-            processes.append(p)
-
-    for p in processes:
-        p.wait()
-        
-def make_parser():
-    usage = '%prog: [options] runfolder'
-
-    parser = OptionParser(usage)
-    
-    parser.add_option('--gerald', 
-                      help='specify location of GERALD directory',
-                      default=None)
-    parser.add_option('-o', '--output',
-                      help='specify output location of files',
-                      default=None)
-    parser.add_option('-l', '--read-length', type='int',
-                      help='specify new eland length',
-                      dest='length',
-                      default=25)
-    parser.add_option('--dry-run', action='store_true',
-                      help='only pretend to run',
-                      default=False)
-    parser.add_option('-v', '--verbose', action='store_true',
-                      help='increase verbosity',
-                      default=False)
-
-    return parser
-
-
-def main(cmdline=None):
-    logging.basicConfig(level=logging.WARNING)
-
-    parser = make_parser()
-    opts, args = parser.parse_args(cmdline)
-
-    if opts.length < 16 or opts.length > 32:
-        parser.error("eland can only process reads in the range 16-32")
-
-    if len(args) > 1:
-        parser.error("Can only process one runfolder directory")
-    elif len(args) == 1:
-        runs = runfolder.get_runs(args[0])
-        if len(runs) != 1:
-            parser.error("Not a runfolder")
-        opts.gerald = runs[0].gerald.pathname
-        if opts.output is None:
-            opts.output = os.path.join(
-                runs[0].pathname, 
-                'Data', 
-                # pythons 0..n ==> elands 1..n+1
-                'C1-%d' % (opts.length+1,) 
-            )
-
-    elif opts.gerald is None:
-        parser.error("need gerald directory")
-    
-    if opts.output is None:
-        parser.error("specify location for the new eland files")
-
-    if opts.verbose:
-        root_logger = logging.getLogger()
-        root_logger.setLevel(logging.INFO)
-
-    rerun(opts.gerald, opts.output, opts.length, dry_run=opts.dry_run)
-
-    return 0
-
-if __name__ == "__main__":
-    sys.exit(main(sys.argv[1:]))