Mercurial > repos > charles_s_test > seqsero

comparison libs/BWA_analysis_O_new_dependent.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
5 from Bio import SeqIO 5 from Bio import SeqIO
6 import sys 6 import sys
7 from Initial_functions import Uniq 7 from Initial_functions import Uniq
8 from Bio.Blast import NCBIXML 8 from Bio.Blast import NCBIXML
9 9
10 BwaPath="/nfs/sw/apps/bwa/bwa-0.7.15/bwa" 10 BwaPath="bwa"
11 SamTlsPth="/nfs/sw/apps/samtools/samtools-1.3.1/bin/samtools" 11 SamTlsPth="samtools"
12 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb" 12 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb"
13 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastn" 13 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastn"
14 14
15 def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode): 15 def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode):
16 if file_mode=="1":#interleaved 16 if file_mode=="1":#interleaved