comparison libs/BWA_analysis_O_new_dependent.py @ 11:b4484db557ab draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

10:53efef402c51

#!/usr/bin/env python
#tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2

import os
from Bio import SeqIO
import sys

    re_core_id=reverse_seq.split(".fastq")[0]
    for_fq=for_core_id+".fastq"
    rev_fq=re_core_id+".fastq"
    dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
    print "check fastq id and make them in accordance with each other...please wait..."
    os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
    for_sai=for_core_id+".sai"
    rev_sai=re_core_id+".sai"
    sam=for_core_id+".sam"
    bam=sam.replace(".sam",".bam")
  elif file_mode=="3":#single-end

11:b4484db557ab

#!/usr/bin/env python2.7
#tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2

import os
from Bio import SeqIO
import sys

    re_core_id=reverse_seq.split(".fastq")[0]
    for_fq=for_core_id+".fastq"
    rev_fq=re_core_id+".fastq"
    dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
    print "check fastq id and make them in accordance with each other...please wait..."
    os.system("python2.7 "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
    for_sai=for_core_id+".sai"
    rev_sai=re_core_id+".sai"
    sam=for_core_id+".sam"
    bam=sam.replace(".sam",".bam")
  elif file_mode=="3":#single-end