# HG changeset patch
# User tyty
# Date 1413783233 14400
# Node ID b0243634fe6b27c03a175326f3ecc0847712e039
# Parent  74ae6f6a3383c4fcc52f962c687d3a0a91478bea
Deleted selected files

diff -r 74ae6f6a3383 -r b0243634fe6b Iterative_mapping/.DS_Store
Binary file Iterative_mapping/.DS_Store has changed
diff -r 74ae6f6a3383 -r b0243634fe6b Iterative_mapping/iterative_map.py
--- a/Iterative_mapping/iterative_map.py	Mon Oct 20 01:33:11 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-import os
-from read_file import *
-from read_s_file import *
-
-type_input = sys.argv[1]
-seq_file = sys.argv[2]
-ref_file = sys.argv[3]
-shift = sys.argv[4]
-length = sys.argv[5]
-map_type = sys.argv[6]
-output_file = sys.argv[7]
-
-
-if map_type!="default":
-    s = ""
-    s = s+"-v "+sys.argv[8]
-    s = s+" -5 "+sys.argv[9]
-    s = s+" -3 "+sys.argv[10]
-    s = s+" -k "+sys.argv[11]
-    if sys.argv[12]:
-        s = s+" -a"
-    if int(sys.argv[13])>=1:
-        s = s+" -m "+sys.argv[13]
-    if sys.argv[14]:
-        s = s+" --best --strata "
-    
-else:
-    s = "-v 3 -a --best --strata "
-
-ospath = os.path.realpath(sys.argv[0])
-ost = ospath.split('/')
-syspath = ""
-for i in range(len(ost)-1):
-    syspath = syspath+ost[i].strip()
-    syspath = syspath+'/'
-
-os.system("bowtie-build -f "+ref_file+" "+syspath+"ref > "+syspath+"log.txt")
-
-os.system("cp "+seq_file+" "+syspath+"seq0.fa")
-
-if type_input == "fasta":
-    tp = 'fasta'
-if type_input == "fastq":
-    tp = 'fastq'
-
-k = 0
-print(type_input)
-while(True):
-    if type_input == "fasta":
-        os.system("bowtie "+s+"-f "+syspath+"ref"+" "+syspath+"seq"+str(k)+".fa --quiet -S > "+syspath+"map"+str(k)+".sam")
-    if type_input == "fastq":
-        os.system("bowtie "+s+"-q "+syspath+"ref"+" "+syspath+"seq"+str(k)+".fa --quiet -S > "+syspath+"map"+str(k)+".sam")
-    os.system("samtools view -Sb -F 0xfff "+syspath+"map"+str(k)+".sam > "+syspath+"mapped"+str(k)+".bam 2>"+syspath+"log.txt") #get mapped reads
-    os.system("samtools view -Sb -f 0x4 "+syspath+"map"+str(k)+".sam > "+syspath+"umapped"+str(k)+".bam 2>"+syspath+"log.txt") #get unmapped reads
-    os.system("samtools view -Sb -f 0x10 "+syspath+"map"+str(k)+".sam > "+syspath+"rmapped"+str(k)+".bam 2>"+syspath+"log.txt") #get reversed mapped reads
-    os.system("samtools merge -f "+syspath+"unmapped"+str(k)+".bam "+syspath+"umapped"+str(k)+".bam "+syspath+"rmapped"+str(k)+".bam") #get reversed mapped reads
-    os.system("samtools view -h -o "+syspath+"unmapped"+str(k)+".sam "+syspath+"unmapped"+str(k)+".bam") #get reversed mapped reads
-    if k>0:
-        os.system("samtools view -h -o "+syspath+"mapped"+str(k)+".sam "+syspath+"mapped"+str(k)+".bam") #get reversed mapped reads
-        os.system("cut -f 1 "+syspath+"unmapped"+str(k)+".sam > "+syspath+"unmapped"+str(k)+".txt")
-        os.system("cut -f 1 "+syspath+"mapped"+str(k)+".sam > "+syspath+"mapped"+str(k)+".txt")
-        os.system("python "+syspath+"remove_map.py "+syspath+"unmapped"+str(k)+".txt "+syspath+"mapped"+str(k)+".txt "+syspath+"runmapped"+str(k)+".txt")
-        os.system("rm "+syspath+"mapped"+str(k)+".sam")
-        os.system("rm "+syspath+"mapped"+str(k)+".txt")
-        os.system("rm "+syspath+"unmapped"+str(k)+".txt")
-    else:
-        os.system("cut -f 1 "+syspath+"unmapped"+str(k)+".sam > "+syspath+"runmapped"+str(k)+".txt")
-    
-    os.system("rm "+syspath+"unmapped"+str(k)+".bam")
-    os.system("rm "+syspath+"umapped"+str(k)+".bam")
-    os.system("rm "+syspath+"rmapped"+str(k)+".bam")
-    os.system("python "+syspath+"seq_track.py "+syspath+"runmapped"+str(k)+".txt "+syspath+"seq"+str(k)+".fa "+syspath+"unmap_seq"+str(k)+".fa "+tp) #get unmapped sequence
-    os.system("python "+syspath+"truncate.py "+syspath+"unmap_seq"+str(k)+".fa "+shift+" "+syspath+"seq"+str(k+1)+".fa "+length) #truncate unmapped sequence
-    os.system("rm "+syspath+"seq"+str(k)+".fa") #Remove sequences being mapped
-    os.system("rm "+syspath+"map"+str(k)+".sam") #Remove mapping file
-    os.system("rm "+syspath+"unmap_seq"+str(k)+".fa") #Remove unmapped sequnce
-    os.system("rm "+syspath+"runmapped"+str(k)+".txt")
-    os.system("rm "+syspath+"unmapped"+str(k)+".sam")
-    
-    os.system("wc -l "+syspath+"seq"+str(k+1)+".fa > "+syspath+"count"+str(k+1)+".txt")
-    c = read_sp_file(syspath+"count"+str(k+1)+".txt")
-    if c[0][0] == '0': #If no reads is in the sequence file, stop
-        os.system("rm "+syspath+"count"+str(k+1)+".txt")
-        os.system("rm "+syspath+"seq"+str(k+1)+".fa")
-        break
-    os.system("rm "+syspath+"count"+str(k+1)+".txt")
-    k = k+1
-
-ss = ""
-for i in range(0,k+1):
-    ss = ss+" "+syspath+"mapped"+str(i)+".bam"
-
-
-os.system("samtools merge -f "+output_file+" "+ss)
-#print("samtools merge mapped_all.bam"+ss)
-os.system("rm "+syspath+"mapped*.bam")
-os.system("rm "+syspath+"ref*")
-
-