Move the code to scan the sequence file archive to its own module so

[htsworkflow.git] / scripts / make-library-tree

diff --git a/scripts/make-library-tree b/scripts/make-library-tree
index b6edb9311eddbd1680fab7bcd86c816ad11c94c9..2ccbec6632717902e3ff2de3513d918952b93cef 100644 (file)
--- a/scripts/make-library-tree
+++ b/scripts/make-library-tree
@@ -6,121 +6,10 @@ import logging
 import os
 from optparse import OptionParser
 import stat
-import re
 import shelve
 
 from htsworkflow.util import api
-
-eland_re = re.compile('s_(?P<lane>\d)(?P<read>_\d)?_eland_')
-raw_seq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Z]+')
-qseq_re = re.compile('woldlab_[0-9]{6}_[^_]+_[\d]+_[\dA-Z]+_l[\d]_r[\d].tar.bz2')
-
-class SequenceFile(object):
-    def __init__(self, filetype, path, flowcell, lane, read=None, pf=None, cycle=None):
-        self.filetype = filetype
-        self.path = path
-        self.flowcell = flowcell
-        self.lane = lane
-        self.read = read
-        self.pf = pf
-        self.cycle = cycle
-
-    def __hash__(self):
-        return hash(self.key())
-
-    def key(self):
-        return (self.flowcell, self.lane)
-
-    def unicode(self):
-        return unicode(self.path)
-
-    def __repr__(self):
-        return u"<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
-
-    def make_target_name(self, root):
-        """
-        Create target name for where we need to link this sequence too
-        """
-        path, basename = os.path.split(self.path)
-        # Because the names aren't unque we include the flowcel name
-        # because there were different eland files for different length
-        # analyses, we include the cycle length in the name.
-        if self.filetype == 'eland':
-            template = "%(flowcell)s_%(cycle)s_%(eland)s"
-            basename = template % { 'flowcell': self.flowcell,
-                                    'cycle': self.cycle,
-                                    'eland': basename }
-        # else:
-        # all the other file types have names that include flowcell/lane
-        # information and thus are unique so we don't have to do anything
-        return os.path.join(root, basename)
-        
-def parse_srf(path, filename):
-    basename, ext = os.path.splitext(filename)
-    records = basename.split('_')
-    flowcell = records[4]
-    lane = int(records[5][0])
-    fullpath = os.path.join(path, filename)
-    return SequenceFile('srf', fullpath, flowcell, lane)
-
-def parse_qseq(path, filename):
-    basename, ext = os.path.splitext(filename)
-    records = basename.split('_')
-    fullpath = os.path.join(path, filename)
-    flowcell = records[4]
-    lane = int(records[5][1])
-    read = int(records[6][1])
-    return SequenceFile('qseq', fullpath, flowcell, lane, read)
-
-def parse_fastq(path, filename):
-    basename, ext = os.path.splitext(filename)
-    records = basename.split('_')
-    fullpath = os.path.join(path, filename)
-    flowcell = records[4]
-    lane = int(records[5][1])
-    read = int(records[6][1])
-    if records[-1] == 'pass':
-        pf = True
-    else:
-        pf = False
-    return SequenceFile('fastq', fullpath, flowcell, lane, read, pf=pf)
-
-def parse_eland(path, filename, eland_match):
-    fullpath = os.path.join(path, filename)
-    rest, cycle = os.path.split(path)
-    rest, flowcell = os.path.split(rest)
-    lane = eland_match.group('lane')
-    read = eland_match.group('read')
-    return SequenceFile('eland', fullpath, flowcell, lane, read, cycle=cycle)
-    
-def scan_for_sequences(dirs):
-    sequences = []
-    for d in dirs:
-        logging.info("Scanning %s for sequences" % (d,))
-        for path, dirname, filenames in os.walk(d):
-            for f in filenames:
-                seq = None
-                # find sequence files
-                if raw_seq_re.match(f):
-                    if f.endswith('.md5'):
-                        continue
-                    elif f.endswith('.srf') or f.endswith('.srf.bz2'):
-                        seq = parse_srf(path, f)
-                    elif qseq_re.match(f):
-                        seq = parse_qseq(path, f)
-                    elif f.endswith('fastq') or f.endswith('.fastq.bz2'):
-                        seq = parse_fastq(path, f)
-                eland_match = eland_re.match(f)
-                if eland_match:
-                    if f.endswith('.md5'):
-                        continue
-                    seq = parse_eland(path, f, eland_match)
-                if seq:
-                    sequences.append(seq)
-                    logging.debug("Found sequence at %s" % (f,))
-                    
-    return sequences
-
+from htsworkflow.pipelines.sequences import scan_for_sequences
 
 def build_flowcell_db(fcdb_filename, sequences, baseurl, apiid, apikey):
     """