TEST_CODE_DIR = os.path.split(__file__)[0]
TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
LANE_LIST = range(1,9)
+TILE_LIST = range(1,101)
def make_firecrest_dir(data_dir, version="1.9.2", start=1, stop=37):
firecrest_dir = os.path.join(data_dir,
f.write(config)
f.close()
-def make_bustard_config132(gerald_dir):
+def make_bustard_config132(image_dir):
source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
- destination = os.path.join(gerald_dir, 'config.xml')
+ destination = os.path.join(image_dir, 'config.xml')
shutil.copy(source, destination)
def make_rta_intensities_1460(data_dir, version='1.4.6.0'):
return basecalls_dir
+def make_qseqs(bustard_dir, in_temp=True):
+ """
+ Fill gerald directory with qseq files
+ """
+ # 42BRJ 8 1 0039 happened to be a better than usual tile, in that there
+ # was actually sequence at the start
+ source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_1_0039_qseq.txt')
+ destdir = bustard_dir
+ if not os.path.isdir(destdir):
+ os.mkdir(destdir)
+
+ for lane in LANE_LIST:
+ for tile in TILE_LIST:
+ destination = os.path.join(bustard_dir, 's_%d_1_%04d_qseq.txt' % (lane, tile))
+ shutil.copy(source, destination)
+
+ make_matrix_dir(bustard_dir)
+ make_phasing_dir(bustard_dir)
+
+ summary_source = os.path.join(TESTDATA_DIR, '42BRJAAXX_BustardSummary.xml')
+ summary_dest = os.path.join(bustard_dir, 'BustardSummary.xml')
+ shutil.copy(summary_source, summary_dest)
+
+ return destdir
+
+def make_scores(gerald_dir, in_temp=True):
+ """
+ Fill gerald directory with score temp files
+ will create the directory if it doesn't exist.
+ """
+ source = os.path.join(TESTDATA_DIR, 's_1_0001_score.txt')
+ destdir = gerald_dir
+ if in_temp:
+ destdir = os.path.join(destdir, 'Temp')
+ if not os.path.isdir(destdir):
+ os.mkdir(destdir)
+
+ for lane in LANE_LIST:
+ for tile in TILE_LIST:
+ destination = os.path.join(destdir, 's_%d_%04d_score.txt' % (lane, tile))
+ shutil.copy(source, destination)
+
+ return destdir
+
+def make_matrix_dir(bustard_dir):
+ """
+ Create several matrix files in <bustard_dir>/Matrix/
+ from pipeline 1.4
+ """
+ destdir = os.path.join(bustard_dir, 'Matrix')
+ if not os.path.isdir(destdir):
+ os.mkdir(destdir)
+
+ source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_02_matrix.txt')
+ for lane in LANE_LIST:
+ destination = os.path.join(destdir, 's_%d_02_matrix.txt' % ( lane, ))
+ shutil.copy(source, destination)
+
def make_matrix(matrix_filename):
contents = """# Auto-generated frequency response matrix
> A
f.write(contents)
f.close()
+def make_phasing_dir(bustard_dir):
+ """
+ Create several phasing files in <bustard_dir>/Phasing/
+
+ from pipeline 1.4
+ """
+ destdir = os.path.join(bustard_dir, 'Phasing')
+ if not os.path.isdir(destdir):
+ os.mkdir(destdir)
+
+ source = os.path.join(TESTDATA_DIR, '42BRJAAXX_8_01_phasing.xml')
+ for lane in LANE_LIST:
+ destination = os.path.join(destdir, 's_%d_01_phasing.xml' % ( lane, ))
+ shutil.copy(source, destination)
+
def make_phasing_params(bustard_dir):
- for lane in range(1,9):
+ for lane in LANE_LIST:
pathname = os.path.join(bustard_dir, 'params%d.xml' % (lane))
f = open(pathname, 'w')
f.write("""<Parameters>
>HWI-EAS229_24_207BTAAXX:1:7:776:582 AGCTCANCCGATCGAAAACCTCNCCAAGCAAT NM 0 0 0
>HWI-EAS229_24_207BTAAXX:1:7:205:842 AAACAANNCTCCCAAACACGTAAACTGGAAAA U1 0 1 0 Lambda.fa 8796855 R DD 24T
"""
- for i in range(1,9):
+ for i in LANE_LIST:
pathname = os.path.join(gerald_dir,
's_%d_eland_result.txt' % (i,))
f = open(pathname, 'w')