[hg] galaxy 1523: Adding tools to compute Substitution rates.

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[hg] galaxy 1523: Adding tools to compute Substitution rates.

greg
details:   http://www.bx.psu.edu/hg/galaxy/rev/dabed25dfbaf
changeset: 1523:dabed25dfbaf
user:      guru
date:      Sun Sep 21 17:36:28 2008 -0400
description:
Adding tools to compute Substitution rates.

7 file(s) affected in this change:

test-data/subRates1.out
test-data/subs.out
tool_conf.xml.sample
tools/regVariation/substitution_rates.py
tools/regVariation/substitution_rates.xml
tools/regVariation/substitutions.py
tools/regVariation/substitutions.xml

diffs (1734 lines):

diff -r 05974294cbf1 -r dabed25dfbaf test-data/subRates1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subRates1.out Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,13 @@
+#Seq1 Start1 End1 Seq2 Start2 End2 L N p
+hg17.chrX 3816458 3816983 fr1.chrUn 343715247 343715776 525 188 0.3581
+hg17.chrX 3795168 3795525 fr1.chrUn 343710815 343711179 357 92 0.2577
+hg17.chrX 3787425 3787599 fr1.chrUn 343708230 343708404 174 37 0.2126
+hg17.chrX 3787284 3787384 fr1.chrUn 62078707 62078816 100 33 0.3300
+hg17.chrX 3776942 3777227 fr1.chrUn 343707053 343707336 283 122 0.4311
+hg17.chrX 3760375 3760468 fr1.chrUn 343706399 343706492 93 20 0.2151
+hg17.chrX 3733405 3733881 fr1.chrUn 303515824 303516268 444 186 0.4189
+hg17.chrX 3731355 3731463 fr1.chrUn 303515724 303515815 91 36 0.3956
+hg17.chrX 3730591 3731038 fr1.chrUn 303515378 303515724 346 126 0.3642
+hg17.chrX 3729219 3729457 fr1.chrUn 343703525 343703763 238 57 0.2395
+hg17.chrX 3700391 3700698 fr1.chrUn 241017738 241018068 307 112 0.3648
+hg17.chrX 3639441 3639646 fr1.chrUn 333536350 333536563 205 66 0.3220
diff -r 05974294cbf1 -r dabed25dfbaf test-data/subs.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/subs.out Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,1379 @@
+#Chr Start End
+hg17.chrX 3816460 3816460
+fr1.chrUn 343715249 343715249
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diff -r 05974294cbf1 -r dabed25dfbaf tool_conf.xml.sample
--- a/tool_conf.xml.sample Sat Sep 20 18:14:24 2008 -0400
+++ b/tool_conf.xml.sample Sun Sep 21 17:36:28 2008 -0400
@@ -128,6 +128,8 @@
     <tool file="regVariation/getIndels_2way.xml" />
     <tool file="regVariation/getIndels_3way.xml" />
     <tool file="regVariation/getIndelRates_3way.xml" />
+    <tool file="regVariation/substitutions.xml" />
+    <tool file="regVariation/substitution_rates.xml" />
   </section>
   <section name="Multiple regression" id="multReg">
     <tool file="regVariation/linear_regression.xml" />
diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitution_rates.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/substitution_rates.py Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,118 @@
+#! /usr/bin/python
+#guruprasad Ananda
+"""
+Estimates substitution rates from pairwise alignments using JC69 model.
+"""
+
+from galaxy import eggs
+from galaxy.tools.util.galaxyops import *
+from galaxy.tools.util import maf_utilities
+import bx.align.maf
+import sys, fileinput
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+if len(sys.argv) < 3:
+        stop_err("Incorrect number of arguments.")    
+    
+inp_file = sys.argv[1]
+out_file = sys.argv[2]
+fout = open(out_file, 'w')
+int_file = sys.argv[3]
+if int_file != "None":     #The user has specified an interval file
+    dbkey_i = sys.argv[4]
+    chr_col_i, start_col_i, end_col_i, strand_col_i = parse_cols_arg( sys.argv[5] )
+
+
+def rateEstimator(block):
+    global alignlen, mismatches
+
+    src1 = block.components[0].src
+    sequence1 = block.components[0].text
+    start1 = block.components[0].start
+    end1 = block.components[0].end
+    len1 = int(end1)-int(start1)
+    len1_withgap = len(sequence1)
+    mismatch = 0.0
+    
+    for seq in range (1,len(block.components)):
+        src2 = block.components[seq].src
+        sequence2 = block.components[seq].text
+        start2 = block.components[seq].start
+        end2 = block.components[seq].end
+        len2 = int(end2)-int(start2)
+        for nt in range(len1_withgap):
+            if sequence1[nt] not in '-#$^*?' and sequence2[nt] not in '-#$^*?': #Not a gap or masked character
+                if sequence1[nt].upper() != sequence2[nt].upper():
+                    mismatch += 1
+    
+    if int_file == "None":  
+        p = mismatch/min(len1,len2)
+        print >>fout, "%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%.4f" %(src1,start1,end1,src2,start2,end2,min(len1,len2),mismatch,p)
+    else:
+        mismatches += mismatch
+        alignlen += min(len1,len2)
+              
+def main():
+    skipped = 0
+    not_pairwise = 0
+    
+    if int_file == "None":
+        try:
+            maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
+        except:
+            stop_err("Your MAF file appears to be malformed.")
+        print >>fout, "#Seq1\tStart1\tEnd1\tSeq2\tStart2\tEnd2\tL\tN\tp"
+        for block in maf_reader:
+            if len(block.components) != 2:
+                not_pairwise += 1
+                continue
+            try:
+                rateEstimator(block)
+            except:
+                skipped += 1
+    else:
+        index, index_filename = maf_utilities.build_maf_index( inp_file, species = [dbkey_i] )
+        if index is None:
+            print >> sys.stderr, "Your MAF file appears to be malformed."
+            sys.exit()
+        win = NiceReaderWrapper( fileinput.FileInput( int_file ),
+                                chrom_col=chr_col_i,
+                                start_col=start_col_i,
+                                end_col=end_col_i,
+                                strand_col=strand_col_i,
+                                fix_strand=True)
+        species=None
+        mincols = 0
+        global alignlen, mismatches
+        
+        for interval in win:
+            alignlen = 0
+            mismatches = 0.0
+            src = "%s.%s" % ( dbkey_i, interval.chrom )
+            for block in maf_utilities.get_chopped_blocks_for_region( index, src, interval, species, mincols ):
+                if len(block.components) != 2:
+                    not_pairwise += 1
+                    continue
+                try:
+                    rateEstimator(block)
+                except:
+                    skipped += 1
+            if alignlen:
+                p = mismatches/alignlen
+            else:
+                p = 'NA'
+            interval.fields.append(str(alignlen))
+            interval.fields.append(str(mismatches))
+            interval.fields.append(str(p))
+            print >>fout, "\t".join(interval.fields)    
+            #num_blocks += 1
+    
+    if not_pairwise:
+        print "Skipped %d non-pairwise blocks" %(not_pairwise)
+    if skipped:
+        print "Skipped %d blocks as invalid" %(skipped)
+if __name__ == "__main__":
+    main()
diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitution_rates.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/substitution_rates.xml Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,61 @@
+<tool id="subRate1" name="Estimate substitution rates " version="1.0.0">
+  <description> for non-coding regions</description>
+  <command interpreter="python">
+   substitution_rates.py
+   $input
+   $out_file1
+   #if $region.type == "win":
+      ${region.input2} ${region.input2.dbkey} ${region.input2.metadata.chromCol},$region.input2.metadata.startCol,$region.input2.metadata.endCol,$region.input2.metadata.strandCol
+    #else:
+      "None"
+    #end if
+  </command>
+  <inputs>
+    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
+    <conditional name="region">
+      <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
+         <option value="align">Alignment block</option>
+         <option value="win">Intervals in your history</option>
+     </param>
+     <when value="win">
+       <param format="interval" name="input2" type="data" label="Choose intervals">
+       <validator type="unspecified_build" />
+     </param>
+      </when>
+      <when value="align" />
+      </conditional>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" metadata_source="input"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
+      <param name="type" value="align"/>
+      <output name="out_file1" file="subRates1.out"/>
+    </test>
+  </tests>
+  
+ <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool takes a pairwise MAF file as input and estimates substitution rate according to Jukes-Cantor JC69 model. The 3 new columns appended to the output are explanied below:
+
+- L: number of nucleotides compared
+- N: number of different nucleotides
+- p = N/L
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+Any block/s not containing exactly two sequences, will be omitted.
+
+  </help>  
+</tool>
\ No newline at end of file
diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitutions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/substitutions.py Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,87 @@
+#! /usr/bin/python
+#Guruprasad ANanda
+"""
+Fetches substitutions from pairwise alignments.
+"""
+
+from galaxy import eggs
+
+from galaxy.tools.util import maf_utilities
+
+import bx.align.maf
+import sys
+import os, fileinput
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+if len(sys.argv) < 3:
+        stop_err("Incorrect number of arguments.")    
+    
+inp_file = sys.argv[1]
+out_file = sys.argv[2]
+fout = open(out_file, 'w')
+
+def fetchSubs(block):
+    
+    src1 = block.components[0].src
+    sequence1 = block.components[0].text
+    start1 = block.components[0].start
+    end1 = block.components[0].end
+    len1 = int(end1)-int(start1)
+    len1_withgap = len(sequence1)
+    
+    for seq in range (1,len(block.components)):
+        src2 = block.components[seq].src
+        sequence2 = block.components[seq].text
+        start2 = block.components[seq].start
+        end2 = block.components[seq].end
+        len2 = int(end2)-int(start2)
+        sub_begin = None
+        sub_end = None
+        begin = False
+        
+        for nt in range(len1_withgap):
+            if sequence1[nt] not in '-#$^*?' and sequence2[nt] not in '-#$^*?': #Not a gap or masked character
+                if sequence1[nt].upper() != sequence2[nt].upper():
+                    if not(begin):
+                        sub_begin = nt
+                        begin = True
+                    sub_end = nt
+                else:
+                    if begin:
+                        print >>fout, "%s\t%s\t%s" %(src1,start1+sub_begin-sequence1[0:sub_begin].count('-'),start1+sub_end-sequence1[0:sub_end].count('-'))
+                        print >>fout, "%s\t%s\t%s" %(src2,start2+sub_begin-sequence2[0:sub_begin].count('-'),start2+sub_end-sequence2[0:sub_end].count('-'))    
+                        begin = False
+
+            else:
+                if begin:
+                    print >>fout, "%s\t%s\t%s" %(src1,start1+sub_begin-sequence1[0:sub_begin].count('-'),end1+sub_end-sequence1[0:sub_end].count('-'))
+                    print >>fout, "%s\t%s\t%s" %(src2,start2+sub_begin-sequence2[0:sub_begin].count('-'),end2+sub_end-sequence2[0:sub_end].count('-'))    
+                    begin = False
+                    ended = False
+    
+              
+def main():
+    skipped = 0
+    not_pairwise = 0
+    try:
+        maf_reader = bx.align.maf.Reader( open(inp_file, 'r') )
+    except:
+        stop_err("Your MAF file appears to be malformed.")
+    print >>fout, "#Chr\tStart\tEnd"
+    for block in maf_reader:
+        if len(block.components) != 2:
+            not_pairwise += 1
+            continue
+        try:
+            fetchSubs(block)
+        except:
+            skipped += 1
+    
+    if not_pairwise:
+        print "Skipped %d non-pairwise blocks" %(not_pairwise)
+    if skipped:
+        print "Skipped %d blocks" %(skipped)
+if __name__ == "__main__":
+    main()
diff -r 05974294cbf1 -r dabed25dfbaf tools/regVariation/substitutions.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/substitutions.xml Sun Sep 21 17:36:28 2008 -0400
@@ -0,0 +1,38 @@
+<tool id="substitutions1" name="Fetch substitutions " version="1.0.0">
+  <description> from pairwise alignments</description>
+  <command interpreter="python">
+   substitutions.py
+   $input
+   $out_file1
+  </command>
+  <inputs>
+    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" metadata_source="input"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
+      <output name="out_file1" file="subs.out"/>
+    </test>
+  </tests>
+ <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool takes a pairwise MAF file as input and fetches substitutions per alignment block.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+Any block/s not containing exactly two sequences, will be omitted.
+
+  </help>  
+</tool>
\ No newline at end of file