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,
'C%d-%d_Firecrest%s_12-04-2008_diane' % (start, stop, version)
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'):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ intensities_dir = os.path.join(data_dir, 'Intensities')
+ if not os.path.exists(intensities_dir):
+ os.mkdir(intensities_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_intensities_config.xml')
+ shutil.copy(param_file, os.path.join(intensities_dir, 'config.xml'))
+
+ return intensities_dir
+
+def make_rta_basecalls_1460(intensities_dir):
+ """
+ Construct an artificial RTA Intensities parameter file and directory
+ """
+ basecalls_dir = os.path.join(intensities_dir, 'BaseCalls')
+ if not os.path.exists(basecalls_dir):
+ os.mkdir(basecalls_dir)
+
+ param_file = os.path.join(TESTDATA_DIR, 'rta_basecalls_config.xml')
+ shutil.copy(param_file, os.path.join(basecalls_dir, 'config.xml'))
+
+ 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')
f.write(eland_result)
f.close()
-def make_eland_multi(gerald_dir, paired=False):
+def make_eland_multi(gerald_dir, paired=False, lane_list=LANE_LIST):
eland_multi = [""">HWI-EAS229_60_30DP9AAXX:1:1:1221:788 AAGATATCTACGACGTGGTATGGCGGTGTCTGGTCGT NM
>HWI-EAS229_60_30DP9AAXX:1:1:931:747 AAAAAAGCAAATTTCATTCACATGTTCTGTGTTCATA 1:0:2 chr5.fa:55269838R0
>HWI-EAS229_60_30DP9AAXX:1:1:1121:379 AGAAGAGACATTAAGAGTTCCTGAAATTTATATCTGG 2:1:0 chr16.fa:46189180R1,chr7.fa:122968519R0,chr8.fa:48197174F0
"""]
if paired:
for e in [1,2]:
- for i in range(1,9):
+ for i in lane_list:
pathname = os.path.join(gerald_dir,
's_%d_%d_eland_multi.txt' % (i,e))
f = open(pathname, 'w')
f.write(eland_multi[e-1])
f.close()
else:
- for i in range(1,9):
+ for i in lane_list:
pathname = os.path.join(gerald_dir,
's_%d_eland_multi.txt' % (i,))
f = open(pathname, 'w')
f.write(eland_multi[0])
f.close()
+
+def make_scarf(gerald_dir, lane_list=LANE_LIST):
+ seq = """HWI-EAS229_92_30VNBAAXX:1:1:0:161:NCAATTACACGACGCTAGCCCTAAAGCTATTTCGAGG:E[aaaabb^a\a_^^a[S`ba_WZUXaaaaaaUKPER
+HWI-EAS229_92_30VNBAAXX:1:1:0:447:NAGATGCGCATTTGAAGTAGGAGCAAAAGATCAAGGT:EUabaab^baabaaaaaaaa^^Uaaaaa\aaaa__`a
+HWI-EAS229_92_30VNBAAXX:1:1:0:1210:NATAGCCTCTATAGAAGCCACTATTATTTTTTTCTTA:EUa`]`baaaaa^XQU^a`S``S_`J_aaaaaabb^V
+HWI-EAS229_92_30VNBAAXX:1:1:0:1867:NTGGAGCAGATATAAAAACAGATGGTGACGTTGAAGT:E[^UaaaUaba^aaa^aa^XV\baaLaLaaaaQVXV^
+HWI-EAS229_92_30VNBAAXX:1:1:0:1898:NAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTGCAA:EK_aaaaaaaaaaaUZaaZaXM[aaaXSM\aaZ]URE
+"""
+ for l in lane_list:
+ pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
+ f = open(pathname,'w')
+ f.write(seq)
+ f.close()
+
+def make_fastq(gerald_dir, lane_list=LANE_LIST):
+ seq = """@HWI-EAS229:1:2:182:712#0/1
+AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
++HWI-EAS229:1:2:182:712#0/1
+\bab_bbaabbababbaaa]]D]bb_baabbab\baa
+@HWI-EAS229:1:2:198:621#0/1
+CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCC
++HWI-EAS229:1:2:198:621#0/1
+[aaaaaaa`_`aaaaaaa[`ZDZaaaaaaaaaaaaaa
+@HWI-EAS229:1:2:209:1321#0/1
+AAAAAAAAAAAAAAAAAAAAANAAAAAAAAAAAAAAA
++HWI-EAS229:1:2:209:1321#0/1
+_bbbbbaaababaabbbbab]D]aaaaaaaaaaaaaa
+"""
+ for l in lane_list:
+ pathname = os.path.join(gerald_dir, 's_%d_sequence.txt' %(l,))
+ f = open(pathname,'w')
+ f.write(seq)
+ f.close()
+
+
projects / htsworkflow.git / blobdiff