logger = logging.getLogger(__name__)
+
class Antibody(models.Model):
antigene = models.CharField(max_length=500, db_index=True)
# New field Aug/20/08
)
catalog = models.CharField(max_length=50, blank=True, null=True)
antibodies = models.CharField(max_length=500, db_index=True)
- source = models.CharField(max_length=500, blank=True, null=True, db_index=True)
+ source = models.CharField(max_length=500,
+ blank=True, null=True, db_index=True)
biology = models.TextField(blank=True, null=True)
notes = models.TextField(blank=True, null=True)
+
def __str__(self):
return '%s - %s' % (self.antigene, self.antibodies)
+
class Meta:
verbose_name_plural = "antibodies"
ordering = ["antigene"]
+
class Cellline(models.Model):
- cellline_name = models.CharField(max_length=100, unique=True, db_index=True)
- nickname = models.CharField(max_length=20,
+ cellline_name = models.CharField(max_length=100,
+ unique=True, db_index=True)
+ nickname = models.CharField(
+ max_length=20,
blank=True,
null=True,
db_index=True)
notes = models.TextField(blank=True)
+
def __str__(self):
return str(self.cellline_name)
class Meta:
ordering = ["cellline_name"]
+
class Condition(models.Model):
condition_name = models.CharField(
max_length=2000, unique=True, db_index=True)
- nickname = models.CharField(max_length=20,
+ nickname = models.CharField(
+ max_length=20,
blank=True,
null=True,
db_index=True,
- verbose_name = 'Short Name')
+ verbose_name='Short Name')
notes = models.TextField(blank=True)
def __str__(self):
class ExperimentType(models.Model):
- name = models.CharField(max_length=50, unique=True)
+ name = models.CharField(max_length=50, unique=True)
+
+ def __str__(self):
+ return str(self.name)
- def __str__(self):
- return str(self.name)
class Tag(models.Model):
- tag_name = models.CharField(max_length=100, db_index=True,blank=False,null=False)
- TAG_CONTEXT = (
- #('Antibody','Antibody'),
- #('Cellline', 'Cellline'),
- #('Condition', 'Condition'),
- ('Library', 'Library'),
- ('ANY','ANY'),
- )
- context = models.CharField(max_length=50,
- choices=TAG_CONTEXT, default='Library')
-
- def __str__(self):
- return '%s' % (self.tag_name)
-
- class Meta:
- ordering = ["context","tag_name"]
+ tag_name = models.CharField(max_length=100,
+ db_index=True,blank=False,null=False)
+ TAG_CONTEXT = (
+ #('Antibody','Antibody'),
+ #('Cellline', 'Cellline'),
+ #('Condition', 'Condition'),
+ ('Library', 'Library'),
+ ('ANY','ANY'),
+ )
+ context = models.CharField(
+ max_length=50,
+ choices=TAG_CONTEXT, default='Library')
+
+ def __str__(self):
+ return '%s' % (self.tag_name,)
+
+ class Meta:
+ ordering = ["context", "tag_name"]
+
class Species(models.Model):
- scientific_name = models.CharField(max_length=256,
- unique=False,
- db_index=True
- )
- common_name = models.CharField(max_length=256, blank=True)
- #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
+ scientific_name = models.CharField(
+ max_length=256,
+ unique=False,
+ db_index=True
+ )
+ common_name = models.CharField(max_length=256, blank=True)
+ #use_genome_build = models.CharField(max_length=100, blank=False, null=False)
- def __str__(self):
- return '%s (%s)' % (self.scientific_name, self.common_name)
+ def __str__(self):
+ return '%s (%s)' % (self.scientific_name, self.common_name)
+
+ class Meta:
+ verbose_name_plural = "species"
+ ordering = ["scientific_name"]
- class Meta:
- verbose_name_plural = "species"
- ordering = ["scientific_name"]
+ @models.permalink
+ def get_absolute_url(self):
+ return ('samples.views.species', [str(self.id)])
- @models.permalink
- def get_absolute_url(self):
- return ('samples.views.species', [str(self.id)])
class Affiliation(models.Model):
- name = models.CharField(max_length=256, db_index=True, verbose_name='Name')
- contact = models.CharField(max_length=256, null=True, blank=True,verbose_name='Lab Name')
- email = models.EmailField(null=True,blank=True)
- users = models.ManyToManyField('HTSUser', null=True, blank=True)
- users.admin_order_field = "username"
-
- def __str__(self):
- name = str(self.name)
- if self.contact is not None and len(self.contact) > 0:
- name += ' ('+self.contact+')'
- return name
-
- def Users(self):
- users = self.users.all().order_by('username')
- return ", ".join([str(a) for a in users ])
-
- class Meta:
- ordering = ["name","contact"]
- unique_together = (("name", "contact"),)
+ name = models.CharField(max_length=256, db_index=True, verbose_name='Name')
+ contact = models.CharField(max_length=256,
+ null=True, blank=True, verbose_name='Lab Name')
+ email = models.EmailField(null=True, blank=True)
+ users = models.ManyToManyField('HTSUser', null=True, blank=True)
+ users.admin_order_field = "username"
+
+ def __str__(self):
+ name = str(self.name)
+ if self.contact is not None and len(self.contact) > 0:
+ name += ' ('+self.contact+')'
+ return name
+
+ def Users(self):
+ users = self.users.all().order_by('username')
+ return ", ".join([str(a) for a in users])
+
+ class Meta:
+ ordering = ["name", "contact"]
+ unique_together = (("name", "contact"),)
+
class LibraryType(models.Model):
- name = models.CharField(max_length=255, unique=True,
- verbose_name="Adapter Type")
- is_paired_end = models.BooleanField(default=True,
- help_text="can you do a paired end run with this adapter")
- can_multiplex = models.BooleanField(default=True,
- help_text="Does this adapter provide multiplexing?")
+ name = models.CharField(max_length=255, unique=True,
+ verbose_name="Adapter Type")
+ is_paired_end = models.BooleanField(
+ default=True,
+ help_text="can you do a paired end run with this adapter")
+ can_multiplex = models.BooleanField(
+ default=True,
+ help_text="Does this adapter provide multiplexing?")
- def __str__(self):
- return str(self.name)
+ def __str__(self):
+ return str(self.name)
- class Meta:
- ordering = ["-id"]
+ class Meta:
+ ordering = ["-id"]
class MultiplexIndex(models.Model):
verbose_name_plural = "multiplex indicies"
unique_together = ('adapter_type', 'multiplex_id')
+
class Library(models.Model):
- id = models.CharField(max_length=10, primary_key=True)
- library_name = models.CharField(max_length=100, unique=True)
- library_species = models.ForeignKey(Species)
- hidden = models.BooleanField(default=False)
- account_number = models.CharField(max_length=100, null=True, blank=True)
- cell_line = models.ForeignKey(Cellline, blank=True, null=True,
- verbose_name="Background")
- condition = models.ForeignKey(Condition, blank=True, null=True)
- antibody = models.ForeignKey(Antibody,blank=True,null=True)
- affiliations = models.ManyToManyField(
- Affiliation,related_name='library_affiliations',null=True)
- tags = models.ManyToManyField(Tag,related_name='library_tags',
- blank=True,null=True)
- REPLICATE_NUM = [(x,x) for x in range(1,7)]
- replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,
- blank=True,null=True)
- experiment_type = models.ForeignKey(ExperimentType)
- library_type = models.ForeignKey(LibraryType, blank=True, null=True,
- verbose_name="Adapter Type")
- multiplex_id = models.CharField(max_length=128,
- blank=True, null=True,
- verbose_name="Index ID")
- creation_date = models.DateField(blank=True, null=True)
- made_for = models.CharField(max_length=50, blank=True,
- verbose_name='ChIP/DNA/RNA Made By')
- made_by = models.CharField(max_length=50, blank=True, default="Lorian")
-
- PROTOCOL_END_POINTS = (
- ('?', 'Unknown'),
- ('Sample', 'Raw sample'),
- ('Progress', 'In progress'),
- ('1A', 'Ligation, then gel'),
- ('PCR', 'Ligation, then PCR'),
- ('1Ab', 'Ligation, PCR, then gel'),
- ('1Ac', 'Ligation, gel, then 12x PCR'),
- ('1Aa', 'Ligation, gel, then 18x PCR'),
- ('2A', 'Ligation, PCR, gel, PCR'),
- ('Done', 'Completed'),
+ id = models.CharField(max_length=10, primary_key=True)
+ library_name = models.CharField(max_length=100, unique=True)
+ library_species = models.ForeignKey(Species)
+ hidden = models.BooleanField(default=False)
+ account_number = models.CharField(max_length=100, null=True, blank=True)
+ cell_line = models.ForeignKey(Cellline, blank=True, null=True,
+ verbose_name="Background")
+ condition = models.ForeignKey(Condition, blank=True, null=True)
+ antibody = models.ForeignKey(Antibody,blank=True,null=True)
+ affiliations = models.ManyToManyField(
+ Affiliation,related_name='library_affiliations',null=True)
+ tags = models.ManyToManyField(Tag,related_name='library_tags',
+ blank=True,null=True)
+ REPLICATE_NUM = [(x,x) for x in range(1,7)]
+ replicate = models.PositiveSmallIntegerField(choices=REPLICATE_NUM,
+ blank=True,null=True)
+ experiment_type = models.ForeignKey(ExperimentType)
+ library_type = models.ForeignKey(LibraryType, blank=True, null=True,
+ verbose_name="Adapter Type")
+ multiplex_id = models.CharField(max_length=128,
+ blank=True, null=True,
+ verbose_name="Index ID")
+ creation_date = models.DateField(blank=True, null=True)
+ made_for = models.CharField(max_length=50, blank=True,
+ verbose_name='ChIP/DNA/RNA Made By')
+ made_by = models.CharField(max_length=50, blank=True, default="Lorian")
+
+ PROTOCOL_END_POINTS = (
+ ('?', 'Unknown'),
+ ('Sample', 'Raw sample'),
+ ('Progress', 'In progress'),
+ ('1A', 'Ligation, then gel'),
+ ('PCR', 'Ligation, then PCR'),
+ ('1Ab', 'Ligation, PCR, then gel'),
+ ('1Ac', 'Ligation, gel, then 12x PCR'),
+ ('1Aa', 'Ligation, gel, then 18x PCR'),
+ ('2A', 'Ligation, PCR, gel, PCR'),
+ ('Done', 'Completed'),
)
- PROTOCOL_END_POINTS_DICT = dict(PROTOCOL_END_POINTS)
- stopping_point = models.CharField(max_length=25,
- choices=PROTOCOL_END_POINTS,
- default='Done')
-
- amplified_from_sample = models.ForeignKey('self',
- related_name='amplified_into_sample',
- blank=True, null=True)
-
- undiluted_concentration = models.DecimalField("Concentration",
- max_digits=5, decimal_places=2, blank=True, null=True,
- help_text = "Undiluted concentration (ng/\u00b5l)")
- # note \u00b5 is the micro symbol in unicode
- successful_pM = models.DecimalField(max_digits=9,
- decimal_places=1, blank=True, null=True)
- ten_nM_dilution = models.BooleanField(default=False)
- gel_cut_size = models.IntegerField(default=225, blank=True, null=True)
- insert_size = models.IntegerField(blank=True, null=True)
- notes = models.TextField(blank=True)
-
- bioanalyzer_summary = models.TextField(blank=True,default="")
- bioanalyzer_concentration = models.DecimalField(max_digits=5,
- decimal_places=2, blank=True, null=True,
- help_text="(ng/\u00b5l)")
- bioanalyzer_image_url = models.URLField(blank=True,default="")
-
- def __str__(self):
- return '#%s: %s' % (self.id, self.library_name)
-
- class Meta:
- verbose_name_plural = "libraries"
- #ordering = ["-creation_date"]
- ordering = ["-id"]
-
- def antibody_name(self):
- str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.label+'</a>'
- return str
- antibody_name.allow_tags = True
-
- def organism(self):
- return self.library_species.common_name
-
- def index_sequences(self):
- """Return a dictionary of multiplex index id to sequence
- Return None if the library can't multiplex,
-
- """
- if self.library_type is None:
- return None
- if not self.library_type.can_multiplex:
- return None
- if self.multiplex_id is None or len(self.multiplex_id) == 0:
- return 'Err: id empty'
- sequences = {}
- multiplex_expressions = self.multiplex_id.split(',')
- for multiplex_term in multiplex_expressions:
- pairs = multiplex_term.split('-')
- if len(pairs) == 1:
- key = pairs[0]
- seq = self._lookup_index(pairs[0])
- elif len(pairs) == 2:
- key = pairs[0] + '-' + pairs[1]
- seq0 = self._lookup_index(pairs[0])
- seq1 = self._lookup_index(pairs[1])
- if seq0 is None or seq1 is None:
- seq = None
- else:
- seq = seq0 + '-' + seq1
- else:
- raise RuntimeError("Too many - seperated sequences")
- if seq is None:
- seq = 'Err: index not found'
- sequences[key] = seq
- return sequences
-
- def _lookup_index(self, multiplex_id):
- try:
- multiplex = MultiplexIndex.objects.get(
- adapter_type = self.library_type.id,
- multiplex_id = multiplex_id)
- return multiplex.sequence
- except MultiplexIndex.DoesNotExist as e:
- return None
-
- def index_sequence_text(self, seperator=' '):
- """Return formatted multiplex index sequences"""
- sequences = self.index_sequences()
- if sequences is None:
- return ""
- if isinstance(sequences, six.string_types):
- return sequences
- multiplex_ids = sequences.keys()
- multiplex_ids.sort()
- return seperator.join(( "%s:%s" %(i,sequences[i]) for i in multiplex_ids))
- index_sequence_text.short_description = "Index"
-
-
- def affiliation(self):
- affs = self.affiliations.all().order_by('name')
- tstr = ''
- ar = []
- for t in affs:
- ar.append(t.__str__())
- return '%s' % (", ".join(ar))
-
- def is_archived(self):
- """
- returns True if archived else False
- """
- if self.longtermstorage_set.count() > 0:
- return True
- else:
- return False
-
- def stopping_point_name(self):
- end_points = Library.PROTOCOL_END_POINTS_DICT
- name = end_points.get(self.stopping_point, None)
- if name is None:
- name = "Lookup Error"
- logger.error("protocol stopping point in database didn't match names in library model")
- return name
-
-
- def libtags(self):
- affs = self.tags.all().order_by('tag_name')
- ar = []
- for t in affs:
- ar.append(t.__str__())
- return '%s' % ( ", ".join(ar))
-
- def DataRun(self):
- str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
- return str
- DataRun.allow_tags = True
-
- def aligned_m_reads(self):
- return getLibReads(self.id)
-
- def aligned_reads(self):
- res = getLibReads(self.id)
-
- # Check data sanity
- if res[2] != "OK":
- return '<div style="border:solid red 2px">'+res[2]+'</div>'
-
- rc = "%1.2f" % (res[1]/1000000.0)
- # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
- if res[0] > 0:
- bgcolor = '#ff3300' # Red
- rc_thr = [10000000,5000000,3000000]
- if self.experiment_type == 'RNA-seq':
- rc_thr = [20000000,10000000,6000000]
-
- if res[1] > rc_thr[0]:
- bgcolor = '#66ff66' # Green
- else:
- if res[1] > rc_thr[1]:
- bgcolor ='#00ccff' # Blue
+ PROTOCOL_END_POINTS_DICT = dict(PROTOCOL_END_POINTS)
+ stopping_point = models.CharField(max_length=25,
+ choices=PROTOCOL_END_POINTS,
+ default='Done')
+
+ amplified_from_sample = models.ForeignKey(
+ 'self',
+ related_name='amplified_into_sample',
+ blank=True, null=True)
+
+ undiluted_concentration = models.DecimalField(
+ "Concentration",
+ max_digits=5, decimal_places=2, blank=True, null=True,
+ help_text="Undiluted concentration (ng/\u00b5l)")
+ # note \u00b5 is the micro symbol in unicode
+ successful_pM = models.DecimalField(
+ max_digits=9, decimal_places=1, blank=True, null=True)
+ ten_nM_dilution = models.BooleanField(default=False)
+ gel_cut_size = models.IntegerField(default=225, blank=True, null=True)
+ insert_size = models.IntegerField(blank=True, null=True)
+ notes = models.TextField(blank=True)
+
+ bioanalyzer_summary = models.TextField(blank=True, default="")
+ bioanalyzer_concentration = models.DecimalField(
+ max_digits=5, decimal_places=2, blank=True, null=True,
+ help_text="(ng/\u00b5l)")
+ bioanalyzer_image_url = models.URLField(blank=True, default="")
+
+ def __str__(self):
+ return '#%s: %s' % (self.id, self.library_name)
+
+ class Meta:
+ verbose_name_plural = "libraries"
+ # ordering = ["-creation_date"]
+ ordering = ["-id"]
+
+ def antibody_name(self):
+ str ='<a target=_self href="/admin/samples/antibody/'+self.antibody.id.__str__()+'/" title="'+self.antibody.__str__()+'">'+self.antibody.label+'</a>'
+ return str
+ antibody_name.allow_tags = True
+
+ def organism(self):
+ return self.library_species.common_name
+
+ def index_sequences(self):
+ """Return a dictionary of multiplex index id to sequence
+ Return None if the library can't multiplex,
+ """
+ if self.library_type is None:
+ return None
+ if not self.library_type.can_multiplex:
+ return None
+ if self.multiplex_id is None or len(self.multiplex_id) == 0:
+ return 'Err: id empty'
+ sequences = {}
+ multiplex_expressions = self.multiplex_id.split(',')
+ for multiplex_term in multiplex_expressions:
+ pairs = multiplex_term.split('-')
+ if len(pairs) == 1:
+ key = pairs[0]
+ seq = self._lookup_index(pairs[0])
+ elif len(pairs) == 2:
+ key = pairs[0] + '-' + pairs[1]
+ seq0 = self._lookup_index(pairs[0])
+ seq1 = self._lookup_index(pairs[1])
+ if seq0 is None or seq1 is None:
+ seq = None
+ else:
+ seq = seq0 + '-' + seq1
+ else:
+ raise RuntimeError("Too many - seperated sequences")
+ if seq is None:
+ seq = 'Err: index not found'
+ sequences[key] = seq
+ return sequences
+
+ def _lookup_index(self, multiplex_id):
+ try:
+ multiplex = MultiplexIndex.objects.get(
+ adapter_type=self.library_type.id,
+ multiplex_id=multiplex_id)
+ return multiplex.sequence
+ except MultiplexIndex.DoesNotExist as e:
+ return None
+
+ def index_sequence_text(self, seperator=' '):
+ """Return formatted multiplex index sequences"""
+ sequences = self.index_sequences()
+ if sequences is None:
+ return ""
+ if isinstance(sequences, six.string_types):
+ return sequences
+ multiplex_ids = sorted(sequences)
+ return seperator.join(("%s:%s" % (i,sequences[i]) for i in multiplex_ids))
+ index_sequence_text.short_description = "Index"
+
+ def affiliation(self):
+ affs = self.affiliations.all().order_by('name')
+ tstr = ''
+ ar = []
+ for t in affs:
+ ar.append(t.__str__())
+ return '%s' % (", ".join(ar))
+
+ def is_archived(self):
+ """returns True if archived else False
+ """
+ if self.longtermstorage_set.count() > 0:
+ return True
else:
- if res[1] > rc_thr[2]:
- bgcolor ='#ffcc33' # Orange
- tstr = '<div style="background-color:'+bgcolor+';color:black">'
- tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
- tstr += '</div>'
- else: tstr = 'not processed yet'
- return tstr
- aligned_reads.allow_tags = True
-
- def public(self):
- SITE_ROOT = '/'
- summary_url = self.get_absolute_url()
- return '<a href="%s">S</a>' % (summary_url,)
- public.allow_tags = True
-
- @models.permalink
- def get_absolute_url(self):
- return ('samples.views.library_to_flowcells', [str(self.id)])
-
- def get_admin_url(self):
- return urlresolvers.reverse('admin:samples_library_change',
- args=(self.id,))
+ return False
+
+ def lanes_sequenced(self):
+ """Count how many lanes of each type were run.
+ """
+ single = 0
+ paired = 1
+ short_read = 0
+ medium_read = 1
+ long_read = 2
+ counts = [[0, 0, 0], [0, 0, 0]]
+
+ for lane in self.lane_set.all():
+ if lane.flowcell.paired_end:
+ lane_type = paired
+ else:
+ lane_type = single
+
+ if lane.flowcell.read_length < 40:
+ read_type = short_read
+ elif lane.flowcell.read_length < 100:
+ read_type = medium_read
+ else:
+ read_type = long_read
+ counts[lane_type][read_type] += 1
+
+ return counts
+
+ def stopping_point_name(self):
+ end_points = Library.PROTOCOL_END_POINTS_DICT
+ name = end_points.get(self.stopping_point, None)
+ if name is None:
+ name = "Lookup Error"
+ logger.error("protocol stopping point in database didn't match names in library model")
+ return name
+
+ def libtags(self):
+ affs = self.tags.all().order_by('tag_name')
+ ar = []
+ for t in affs:
+ ar.append(t.__str__())
+ return '%s' % (", ".join(ar))
+
+ def DataRun(self):
+ str ='<a target=_self href="/admin/experiments/datarun/?q='+self.id+'" title="Check All Data Runs for This Specific Library ..." ">Data Run</a>'
+ return str
+ DataRun.allow_tags = True
+
+ def aligned_m_reads(self):
+ return getLibReads(self.id)
+
+ def aligned_reads(self):
+ res = getLibReads(self.id)
+
+ # Check data sanity
+ if res[2] != "OK":
+ return '<div style="border:solid red 2px">'+res[2]+'</div>'
+
+ rc = "%1.2f" % (res[1]/1000000.0)
+ # Color Scheme: green is more than 10M, blue is more than 5M, orange is more than 3M and red is less. For RNAseq, all those thresholds should be doubled
+ if res[0] > 0:
+ bgcolor = '#ff3300' # Red
+ rc_thr = [10000000, 5000000, 3000000]
+ if self.experiment_type == 'RNA-seq':
+ rc_thr = [20000000, 10000000, 6000000]
+
+ if res[1] > rc_thr[0]:
+ bgcolor = '#66ff66' # Green
+ else:
+ if res[1] > rc_thr[1]:
+ bgcolor = '#00ccff' # Blue
+ else:
+ if res[1] > rc_thr[2]:
+ bgcolor = '#ffcc33' # Orange
+ tstr = '<div style="background-color:'+bgcolor+';color:black">'
+ tstr += res[0].__str__()+' Lanes, '+rc+' M Reads'
+ tstr += '</div>'
+ else:
+ tstr = 'not processed yet'
+ return tstr
+ aligned_reads.allow_tags = True
+
+ def public(self):
+ summary_url = self.get_absolute_url()
+ return '<a href="%s">S</a>' % (summary_url,)
+ public.allow_tags = True
+
+ @models.permalink
+ def get_absolute_url(self):
+ return ('samples.views.library_to_flowcells', [str(self.id)])
+
+ def get_admin_url(self):
+ return urlresolvers.reverse('admin:samples_library_change',
+ args=(self.id,))
+
class HTSUser(User):
"""
return '/admin/%s/%s/%d' % (self._meta.app_label, self._meta.module_name, self.id)
def __str__(self):
- #return str(self.username) + " (" + str(self.get_full_name()) + u")"
+ # return str(self.username) + " (" + str(self.get_full_name()) + u")"
return str(self.get_full_name()) + ' (' + str(self.username) + ')'
def HTSUserInsertID(sender, instance, **kwargs):
projects / htsworkflow.git / commitdiff