Mercurial > repos > charles_s_test > seqsero2

comparison libs/BWA_analysis_O_new_dependent.py @ 3:38ad1130d077 draft

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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
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="bwa" 10 BwaPath="bwa"
11 SamTlsPth="samtools" 11 SamTlsPth="samtools"
12 Makebltdb="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/makeblastdb" 12 Makebltdb="makeblastdb"
13 Blastnpth="/nfs/sw/apps/blast/ncbi-blast-2.6.0+/bin/blastn" 13 Blastnpth="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
17 if sra_name[-3:]=="sra": 17 if sra_name[-3:]=="sra":
18 os.system("fastq-dump --split-files "+sra_name) 18 os.system("fastq-dump --split-files "+sra_name)