TEST_CODE_DIR = os.path.split(__file__)[0]
TESTDATA_DIR = os.path.join(TEST_CODE_DIR, 'testdata')
-
+LANE_LIST = range(1,9)
+
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(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()
+
+