Mercurial > repos > charles_s_test > seqsero2
comparison libs/deletion_compare.py @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
|---|---|
| date | Mon, 27 Nov 2017 11:21:07 -0500 |
| parents | 0d65b71ff8df |
| children | 3d6680af0bec |
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| 2:0d65b71ff8df | 3:38ad1130d077 |
|---|---|
| 5 from Initial_functions import Uniq | 5 from Initial_functions import Uniq |
| 6 from Bio.Blast import NCBIXML | 6 from Bio.Blast import NCBIXML |
| 7 | 7 |
| 8 BwaPath="bwa" | 8 BwaPath="bwa" |
| 9 SamTlsPth="samtools" | 9 SamTlsPth="samtools" |
| 10 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb" | 10 Makebltdb="makeblastdb" |
| 11 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastn" | 11 Blastnpth="blastn" |
| 12 | 12 |
| 13 target=sys.argv[1] #should be sra format | 13 target=sys.argv[1] #should be sra format |
| 14 test_gene=sys.argv[2] | 14 test_gene=sys.argv[2] |
| 15 mapping_mode=sys.argv[3] | 15 mapping_mode=sys.argv[3] |
| 16 if sys.argv[4] not in ("1","2","3"): | 16 if sys.argv[4] not in ("1","2","3"): |