Mercurial > repos > tyty > structurefold
comparison Iterative_mapping/iterative_map.py @ 112:87ec0ecdc2af draft
Uploaded
| author | tyty |
|---|---|
| date | Sun, 12 Apr 2015 14:28:30 -0400 |
| parents | b6bdd41440f3 |
| children |
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| 111:9c57713215bb | 112:87ec0ecdc2af |
|---|---|
| 101 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") | 101 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") |
| 102 os.system("rm "+syspathrs+"seq"+str(k+1)+".fa") | 102 os.system("rm "+syspathrs+"seq"+str(k+1)+".fa") |
| 103 break | 103 break |
| 104 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") | 104 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") |
| 105 k = k+1 | 105 k = k+1 |
| 106 if type_input == "fasta": | 106 os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam") |
| 107 os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam") | |
| 108 if type_input == "fastq": | |
| 109 os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam") | |
| 110 | 107 |
| 111 | 108 |
| 112 ss = "" | 109 ss = "" |
| 113 for i in range(0,k+1): | 110 for i in range(0,k+1): |
| 114 ss = ss+" "+syspathrs+"mapped"+str(i)+".bam" | 111 ss = ss+" "+syspathrs+"mapped"+str(i)+".bam" |