--- /dev/null
+"""Standardize reading and writing fastq submission names.
+"""
+import collections
+import re
+PAIRED_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}_r{read}.fastq'
+SINGLE_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}.fastq'
+
+FASTQ_RE = re.compile(
+ '(?P<lib_id>[^_]+)_(?P<flowcell>[^_]+)_'\
+ 'c(?P<cycle>[\d]+)_l(?P<lane>[\d]+)(_r(?P<read>[\d]))?\.fastq')
+
+class FastqName(collections.Mapping):
+ def __init__(self, is_paired=None, **kwargs):
+ self._attributes = ('flowcell', 'lib_id', 'lane', 'read', 'cycle')
+ self._is_paired = is_paired
+
+ if len(kwargs) == 0:
+ return
+ if 'filename' in kwargs:
+ self._init_by_filename(**kwargs)
+ else:
+ self._init_by_attributes(**kwargs)
+
+ def _init_by_attributes(self, **kwargs):
+ for k in self._attributes:
+ value = None
+ if k in kwargs:
+ value = kwargs[k]
+ self[k] = value
+
+
+ def _init_by_filename(self, filename):
+ match = FASTQ_RE.match(filename)
+ if match is None:
+ raise ValueError('Is "{0}" a submission fastq?'.format(filename))
+
+ for k in self._attributes:
+ self[k] = match.group(k)
+
+ def _get_is_paired(self):
+ if self._is_paired is None:
+ return getattr(self, 'read', None) is not None
+ else:
+ return self._is_paired
+ def _set_is_paired(self, value):
+ self._is_paired = value
+ is_paired = property(_get_is_paired, _set_is_paired)
+
+ def _is_valid(self):
+ if self.is_paired and self['read'] is None:
+ return False
+
+ for k in self.keys():
+ if k == 'read':
+ continue
+ if self[k] is None:
+ return False
+ return True
+ is_valid = property(_is_valid)
+
+ def _get_filename(self):
+ if not self.is_valid:
+ raise ValueError(
+ "Please set all needed variables before generating a filename")
+
+ T = PAIRED_TEMPLATE if self.is_paired else SINGLE_TEMPLATE
+ return T.format(**self)
+ filename = property(_get_filename)
+
+ def __iter__(self):
+ return iter(self._attributes)
+
+ def __getitem__(self, key):
+ return getattr(self, key, None)
+
+ def __setitem__(self, key, value):
+ if key in self._attributes:
+ setattr(self, key, value)
+ else:
+ raise ValueError("Unrecognized key {0}".format(key))
+
+ def __len__(self):
+ return len([k for k in self if self[k] is not None])
--- /dev/null
+from unittest2 import TestCase
+from htsworkflow.submission.fastqname import FastqName
+
+class TestFastqName(TestCase):
+ def test_init_empty(self):
+ fq = FastqName()
+ self.assertEqual(fq.is_valid, False)
+
+ def test_init_single_filename(self):
+ fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq")
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_single_filename(self):
+ fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.read, "2")
+ self.assertEqual(fq['read'], "2")
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_bad_filename(self):
+ attribs = {'filename': 'asdf.bam'}
+ self.assertRaises(ValueError, FastqName, **attribs)
+
+ def test_init_single_attributes(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1")
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.is_paired, False)
+ self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
+
+ def test_init_single_attributes_set_single(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", is_paired=False)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_single_attributes_set_paired(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", is_paired=True)
+ self.assertEqual(fq.is_valid, False)
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_paired_attributes(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2")
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.lib_id, "12345")
+ self.assertEqual(fq['lib_id'], "12345")
+ self.assertEqual(fq.flowcell, "AABBCCDDXX")
+ self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+ self.assertEqual(fq.cycle, "100")
+ self.assertEqual(fq['cycle'], "100")
+ self.assertEqual(fq.lane, "1")
+ self.assertEqual(fq['lane'], "1")
+ self.assertEqual(fq.read, "2")
+ self.assertEqual(fq['read'], "2")
+ self.assertEqual(fq.is_paired, True)
+ self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1_r2.fastq")
+
+ def test_init_paired_attributes_set_single(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2", is_paired=False)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, False)
+
+ def test_init_paired_attributes_set_paired(self):
+ fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+ cycle = "100", lane="1", read="2", is_paired=True)
+ self.assertEqual(fq.is_valid, True)
+ self.assertEqual(fq.is_paired, True)
+
+ def test_init_insufficient_attributes(self):
+ attribs = dict(lib_id="12345", flowcell="AABBCCDDXX")
+ fq = FastqName(**attribs)
+ self.assertEqual(fq.is_valid, False)
+
+
+def suite():
+ from unittest2 import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
+ return suite
+
+if __name__ == "__main__":
+ from unittest2 import main
+ main(defaultTest='suite')