Mercurial > repos > charles_s_test > seqsero2

comparison libs/deletion_compare.py @ 2:0d65b71ff8df draft

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planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6
author charles_s_test
date Sun, 12 Nov 2017 02:27:32 -0500
parents 6895de35a263
children 38ad1130d077
comparison
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1:8cd7fc65c3a7 2:0d65b71ff8df
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]