summary_dest = os.path.join(paths.summary_dir, 'Sample_Summary.htm')
shutil.copy(summary_source, summary_dest)
- body = get_unaligned_sample_export(lane, index_seq)
+ body = get_aligned_sample_export(lane, index_seq)
for split in ['001','002']:
for read in UNALIGNED_READS:
suffix = 'R{0}_{1}_export.txt.gz'.format(read, split)
""".format(flowcell=flowcell_id, lane=lane, index=index_seq)
return seq
-def get_unaligned_sample_export(lane, index_seq):
+def get_aligned_sample_export(lane, index_seq):
body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t
-HWI-ST0787\t102 {lane} 1101 1478 1997 {index} 1 CAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N
-HWI-ST0787 102 {lane} 1101 1625 1994 {index} 1 AANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA \^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c chrII.fa
+HWI-ST0787\t102\t{lane}\t1101\t1478\t1997\t{index}\t1\tCAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT\tBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\tNM\t\t\t\t\t\t\t\t\t\t\tN
+HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\tchrII.fa\t67717938\tR\t99\t72
+HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\t3:4:3\t\t\t\t\t\t\t\t\t\t\tY
""".format(lane=lane, index=index_seq)
return body