Mercurial > repos > charles_s_test > seqsero

comparison libs/deletion_compare.py @ 2:381e1e7109fc draft default tip

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planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6-dirty
author charles_s_test
date Sun, 12 Nov 2017 02:26:17 -0500
parents 8db411fab3e1
children
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1:139f1e77d834 2:381e1e7109fc
3 from Bio import SeqIO 3 from Bio import SeqIO
4 import sys 4 import sys
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="/nfs/sw/apps/bwa/bwa-0.7.15/bwa" 8 BwaPath="bwa"
9 SamTlsPth="/nfs/sw/apps/samtools/samtools-1.3.1/bin/samtools" 9 SamTlsPth="samtools"
10 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb" 10 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb"
11 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastn" 11 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/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]