From 4509f042c39705140aaba8d2cf5ecc32e350263b Mon Sep 17 00:00:00 2001 From: Brandon King Date: Sat, 17 Nov 2007 01:28:51 +0000 Subject: [PATCH] [project @ Use genome build patch] * WARNING: Changed DB model! (adds use_genome_build to species) * Update to django model to support proper generation of eland config files * Config file now generates config file with the following pattern: * %(Homo sapiens|hg18)s for the run daemon to decide if that genome is available or not. --- ga_frontend/eland_config/views.py | 26 +++++++++++++++++--------- ga_frontend/fctracker/models.py | 6 ++++-- 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/ga_frontend/eland_config/views.py b/ga_frontend/eland_config/views.py index b87fdf9..596e0ff 100644 --- a/ga_frontend/eland_config/views.py +++ b/ga_frontend/eland_config/views.py @@ -316,21 +316,29 @@ def getElandConfig(flowcell, regenerate=False): genome_dict = {} #l1s = form['lane1_species'] - l1s = fcObj.lane_1_library.library_species.scientific_name + l1s = fcObj.lane_1_library.library_species.scientific_name + '|' + \ + fcObj.lane_1_library.library_species.use_genome_build genome_dict.setdefault(l1s, []).append('1') - l2s = fcObj.lane_2_library.library_species.scientific_name + l2s = fcObj.lane_2_library.library_species.scientific_name + '|' + \ + fcObj.lane_2_library.library_species.use_genome_build genome_dict.setdefault(l2s, []).append('2') - l3s = fcObj.lane_3_library.library_species.scientific_name + l3s = fcObj.lane_3_library.library_species.scientific_name + '|' + \ + fcObj.lane_3_library.library_species.use_genome_build genome_dict.setdefault(l3s, []).append('3') - l4s = fcObj.lane_4_library.library_species.scientific_name + l4s = fcObj.lane_4_library.library_species.scientific_name + '|' + \ + fcObj.lane_4_library.library_species.use_genome_build genome_dict.setdefault(l4s, []).append('4') - l5s = fcObj.lane_5_library.library_species.scientific_name + l5s = fcObj.lane_5_library.library_species.scientific_name + '|' + \ + fcObj.lane_5_library.library_species.use_genome_build genome_dict.setdefault(l5s, []).append('5') - l6s = fcObj.lane_6_library.library_species.scientific_name + l6s = fcObj.lane_6_library.library_species.scientific_name + '|' + \ + fcObj.lane_6_library.library_species.use_genome_build genome_dict.setdefault(l6s, []).append('6') - l7s = fcObj.lane_7_library.library_species.scientific_name + l7s = fcObj.lane_7_library.library_species.scientific_name + '|' + \ + fcObj.lane_7_library.library_species.use_genome_build genome_dict.setdefault(l7s, []).append('7') - l8s = fcObj.lane_8_library.library_species.scientific_name + l8s = fcObj.lane_8_library.library_species.scientific_name + '|' + \ + fcObj.lane_8_library.library_species.use_genome_build genome_dict.setdefault(l8s, []).append('8') genome_list = genome_dict.keys() @@ -341,7 +349,7 @@ def getElandConfig(flowcell, regenerate=False): lanes = ''.join(genome_dict[genome]) data.append('%s:ANALYSIS eland' % (lanes)) data.append('%s:READ_LENGTH %s' % (lanes, read_length)) - data.append('%s:ELAND_GENOME %s' % (lanes, os.path.join(BASE_DIR, genome))) + data.append('%s:ELAND_GENOME %s' % (lanes, '%%(%s)s' % (genome))) data.append('%s:USE_BASES %s' % (lanes, 'Y'*int(read_length))) data.append('SEQUENCE_FORMAT --scarf') diff --git a/ga_frontend/fctracker/models.py b/ga_frontend/fctracker/models.py index e86183c..013f36b 100644 --- a/ga_frontend/fctracker/models.py +++ b/ga_frontend/fctracker/models.py @@ -7,9 +7,10 @@ class Species(models.Model): scientific_name = models.CharField(max_length=256, unique=True, db_index=True, core=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) + return '%s (%s)|%s' % (self.scientific_name, self.common_name, self.use_genome_build) class Meta: verbose_name_plural = "species" @@ -18,7 +19,7 @@ class Species(models.Model): class Admin: fields = ( (None, { - 'fields': (('scientific_name', 'common_name'),) + 'fields': (('scientific_name', 'common_name'), ('use_genome_build')) }), ) @@ -27,6 +28,7 @@ class Library(models.Model): library_id = models.IntegerField(primary_key=True, db_index=True, core=True) library_name = models.CharField(max_length=100, unique=True, core=True) library_species = models.ForeignKey(Species, core=True) + #use_genome_build = models.CharField(max_length=100, blank=False, null=False) RNAseq = models.BooleanField() made_by = models.CharField(max_length=50, blank=True, default="Lorian") -- 2.30.2