# HG changeset patch
# User tyty
# Date 1410806521 14400
# Node ID b6d9b0059499f305501ca5d442900410b13f01c0
# Parent d56631911cc16db2c852e30f8db287717eb1897a
Deleted selected files
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/.DS_Store
Binary file Iterative_mapping/.DS_Store has changed
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/iterative_map.py
--- a/Iterative_mapping/iterative_map.py Mon Sep 15 14:41:13 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*")
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/iterative_map.xml
--- a/Iterative_mapping/iterative_map.xml Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-
-
-
- #if $mapping_file.type == "user"
- iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best
- #else
- iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output
- #end if
-
-
- biopython
- numpy
- samtools
- bowtie
-
-
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-
-**TIPS**:
-
------
-
-**Input**:
-
-* 1. Sequence file type (FASTA/FASTQ)
-* 2. Sequence file (fasta/fastq format) {Default: fastq file}
-* 3. Reference file (e.g. cDNA library [fasta])
-* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
-* 5. “Length” (The minimum length of the reads for mapping after trimming)
-* [Optional]
-* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. use -5/-3 flag to trim nucleotides from 5'/3' end of the reads)
-
------
-
-**Output**:
-
-A bam file with all of the reads that are mapped
-
-
-
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/map_ex.py
--- a/Iterative_mapping/map_ex.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
- tline = aline.strip();
- tl = tline.split('\t');
- if len(tl)>4:
- if int(tl[1].strip())== 0:
- h.write(tline)
- h.write('\n')
-
-
-f.close();
-h.close()
-
-
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/read_file.py
--- a/Iterative_mapping/read_file.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_t_file(in_file):
- f = open(in_file);
- result = [];
- for aline in f.readlines():
- temp = [];
- tline = aline.strip();
- tl = tline.split('\t');
- for i in range(0, len(tl)):
- temp.append(tl[i].strip());
- result.append(temp);
- f.close();
- return result;
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/read_s_file.py
--- a/Iterative_mapping/read_s_file.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-
-
-
-def read_sp_file(in_file):
- f = open(in_file);
- result = [];
- for aline in f.readlines():
- temp = [];
- tline = aline.strip();
- tl = tline.split(' ');
- for i in range(0, len(tl)):
- if len(tl[i].strip())>0:
- temp.append(tl[i].strip());
- result.append(temp);
- f.close();
- return result;
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/remove_map.py
--- a/Iterative_mapping/remove_map.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-
-
-unmap_file = sys.argv[1]
-map_file = sys.argv[2]
-result_file = sys.argv[3]
-
-
-unmap = read_t_file(unmap_file)
-mapped = read_t_file(map_file)
-h = file(result_file, 'w')
-
-maps = set()
-for i in range(len(mapped)):
- maps.add(mapped[i][0])
-
-
-for i in range(len(unmap)):
- name = unmap[i][0]
- if name not in maps:
- h.write(name)
- h.write('\n')
-
-
-h.close()
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/seq_track.py
--- a/Iterative_mapping/seq_track.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-unmap_file = sys.argv[1]
-reads_file = sys.argv[2]
-result_file = sys.argv[3]
-tp = sys.argv[4]
-
-
-unmap = read_t_file(unmap_file);
-
-h = file(result_file, 'w')
-
-reads = SeqIO.parse(reads_file,tp)
-um = set()
-for i in range(0, len(unmap)):
- id_r = unmap[i][0]
- um.add(id_r)
-
-for read in reads:
- if read.id in um:
- h.write('>')
- h.write(read.id)
- h.write('\n')
- h.write(read.seq.tostring())
- h.write('\n')
-
-
-
-h.close()
-
-
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/tool_dependencies.xml
--- a/Iterative_mapping/tool_dependencies.xml Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
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diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/truncate.py
--- a/Iterative_mapping/truncate.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from Bio import SeqIO
-
-fasta_file = sys.argv[1]
-shift_in = sys.argv[2]
-result_file = sys.argv[3]
-length = sys.argv[4]
-
-shift = int(shift_in)
-
-fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
-h = file(result_file,'w')
-for seq in fasta_sequences:
- nuc = seq.id;
- sequence = seq.seq.tostring();
- if (len(sequence)-shift)>=int(length):
- h.write('>'+nuc)
- h.write('\n')
- h.write(sequence[0:(len(sequence)-shift)])
- h.write('\n')
-
-
-
-
-h.close()
-
-
-
-
diff -r d56631911cc1 -r b6d9b0059499 Iterative_mapping/unmap.py
--- a/Iterative_mapping/unmap.py Mon Sep 15 14:41:13 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-from read_file import *
-from Bio import SeqIO
-
-map_file = sys.argv[1]
-result_file = sys.argv[2]
-
-
-#reads = read_t_file(read_file);
-
-f = open(map_file);
-h = file(result_file, 'w')
-
-for aline in f.readlines():
- tline = aline.strip();
- tl = tline.split('\t');
- if len(tl)>4:
- if int(tl[1].strip()) != 0:
- h.write(tl[0].strip());
- h.write('\n');
-
-
-f.close();
-h.close()
-
-
-
-