Add building srf files to runfolder as part of --extract-results

[htsworkflow.git] / scripts / srf

diff --git a/scripts/srf b/scripts/srf
index e7478a9d5ff38da60eb26393cc0a9ba50eb0264e..5a06d5d9af24ddb491a5f5c79b7c79137355eff6 100644 (file)
--- a/scripts/srf
+++ b/scripts/srf
@@ -1,72 +1,13 @@
 #!/usr/bin/python
 
-from glob import glob
 import logging
 import optparse
 import os
-import subprocess
 import sys
 
-from htsworkflow.util import queuecommands
 from htsworkflow.pipelines import runfolder
-
-SOLEXA2SRF = 0
-ILLUMINA2SRF10 = 1
-ILLUMINA2SRF11 = 2
-
-def make_commands(run_name, lanes, site_name, destdir, cmdlevel=ILLUMINA2SRF11):
-  """
-  make a subprocess-friendly list of command line arguments to run solexa2srf
-  generates files like: 
-  woldlab:080514_HWI-EAS229_0029_20768AAXX:8.srf
-   site        run name                    lane
-             
-  run_name - most of the file name (run folder name is a good choice)
-  lanes - list of integers corresponding to which lanes to process
-  site_name - name of your "sequencing site" or "Individual"
-  destdir - where to write all the srf files
-  """
-  cmd_list = []
-  for lane in lanes:
-    name_prefix = '%s_%%l_%%t_' % (run_name,)
-    destname = '%s_%s_%d.srf' % (site_name, run_name, lane)
-    destdir = os.path.normpath(destdir)
-    dest_path = os.path.join(destdir, destname)
-    seq_pattern = 's_%d_*_seq.txt' % (lane,)
-
-    if cmdlevel == SOLEXA2SRF:
-        cmd = ['solexa2srf', 
-               '-N', name_prefix,
-               '-n', '%3x:%3y', 
-               '-o', dest_path, 
-               seq_pattern]
-    elif cmdlevel == ILLUMINA2SRF10:
-        cmd = ['illumina2srf', 
-               '-v1.0',
-               '-o', dest_path,
-               seq_pattern]
-    elif cmdlevel == ILLUMINA2SRF11:
-        seq_pattern = 's_%d_*_qseq.txt' % (lane,)
-        cmd = ['illumina2srf', 
-               '-o', dest_path,
-               seq_pattern]
-    else:
-        raise ValueError("Unrecognized run level %d" % (cmdlevel,))
-
-    cmd_list.append(" ".join(cmd))
-  return cmd_list
-
-def pathname_to_run_name(base):
-  """
-  Convert a pathname to a base runfolder name
-  handle the case with a trailing /
-  """
-  name = ""
-  while len(name) == 0:
-    base, name = os.path.split(base)
-    if len(base) == 0:
-      return None
-  return name
+from htsworkflow.pipelines.srf import make_commands, run_srf_commands
+from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF
 
 def make_parser():
   usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'
@@ -149,8 +90,7 @@ def main(cmdline=None):
     for runfolder_path, lanes in zip(args, lanes_list):
         # normalize paths, either relative to home dirs or current dir
         runfolder_path = os.path.abspath(runfolder_path)
-        # the last part of the path should be a runfolder name
-        name = pathname_to_run_name(runfolder_path)
+        run_name = pathname_to_run_name(runfolder_path)
         # so any bustard directories?
         runs = runfolder.get_runs(runfolder_path)
         # give up if there are anything other than 1 run
@@ -159,18 +99,14 @@ def main(cmdline=None):
           return 1
         elif len(runs) == 1:
           bustard_dir = runs[0].bustard.pathname
-          cmds[bustard_dir] = make_commands(name, lanes, opts.site, opts.dest_dir, opts.runfolder_version)
+          cmds[bustard_dir] = make_commands(run_name, lanes, opts.site, opts.dest_dir, opts.runfolder_version)
         else:
           print "ERROR: Couldn't find a bustard directory in", runfolder_path
           return 1
 
     if not opts.dry_run:
       for cwd, cmd_list in cmds.items():
-        curdir = os.getcwd()
-        os.chdir(cwd)
-        q = queuecommands.QueueCommands(cmd_list, opts.jobs)
-        q.run()
-        os.chdir(curdir)
+        run_srf_command(cwd, cmd_list, opts.jobs)
     else:
       for cwd, cmd_list in cmds.items():
         print cwd