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changeset 1:b6d9b0059499 draft

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Deleted selected files
author tyty
date Mon, 15 Sep 2014 14:42:01 -0400
parents d56631911cc1
children 297cdb01d656
files Iterative_mapping/.DS_Store Iterative_mapping/iterative_map.py Iterative_mapping/iterative_map.xml Iterative_mapping/map_ex.py Iterative_mapping/read_file.py Iterative_mapping/read_s_file.py Iterative_mapping/remove_map.py Iterative_mapping/seq_track.py Iterative_mapping/tool_dependencies.xml Iterative_mapping/truncate.py Iterative_mapping/unmap.py
diffstat 11 files changed, 0 insertions(+), 402 deletions(-) [+]
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Binary file Iterative_mapping/.DS_Store has changed
--- 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*")
-
-
--- 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 @@
-<tool id="iterative_map_pipeline" name="Iterative mapping" version="1.0">
-	<description></description>
-	<command interpreter="python">
-        #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
-    </command>
-        <requirements>
-                <requirement type="package" version="1.61">biopython</requirement>
-                <requirement type="package" version="1.7">numpy</requirement>
-                <requirement type="package" version="0.1.18">samtools</requirement>
-                <requirement type="package" version="0.12.7">bowtie</requirement>
-        </requirements>
-	<inputs>
-                <conditional name="file_format">
-                  <param name="type" type="select" label="Format of the file of the reads (Default FASTQ)">
-                    <option value="fastq">FASTQ</option>
-                    <option value="fasta">FASTA</option>
-                  </param>
-                  <when value="fastq">
-                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
-                  </when>
-                  <when value="fasta">
-                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
-                  </when>
-                </conditional>
-		<param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
-                <param name="shift" type="integer" value="1" label="Number of nucleotide trimmed each round"/>
-                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
-                <conditional name="mapping_file">
-                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
-                    <option value="default">Default</option>
-                    <option value="user">User specified</option>
-                  </param>
-                  <when value="default"/>
-                  <when value="user"> 
-                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
-                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
-                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
-                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
-                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
-                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
-                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
-                  </when>
-                </conditional>
-
-	</inputs>
-	<outputs>
-		<data name="output" type="data" format="bam"/>
-	</outputs>
-
-	<help>
-
-
-**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	
-
-
-
-	</help>
-</tool>
--- 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()
-
-
-
-
--- 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;
-
-
--- 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;
-
-
--- 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()
--- 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()
-
-
-
-
--- 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 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="biopython" version="1.61">
-        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7">
-        <repository changeset_revision="4:ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- 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()
-
-
-
-
--- 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()
-
-
-
-