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 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333536475 +hg17.chrX 3639563 3639564 +fr1.chrUn 333536480 333536481 +hg17.chrX 3639572 3639572 +fr1.chrUn 333536489 333536489 +hg17.chrX 3639576 3639577 +fr1.chrUn 333536493 333536494 +hg17.chrX 3639579 3639579 +fr1.chrUn 333536496 333536496 +hg17.chrX 3639588 3639588 +fr1.chrUn 333536505 333536505 +hg17.chrX 3639592 3639592 +fr1.chrUn 333536509 333536509 +hg17.chrX 3639598 3639598 +fr1.chrUn 333536515 333536515 +hg17.chrX 3639600 3639600 +fr1.chrUn 333536517 333536517 +hg17.chrX 3639603 3639603 +fr1.chrUn 333536520 333536520 +hg17.chrX 3639606 3639606 +fr1.chrUn 333536523 333536523 +hg17.chrX 3639612 3639612 +fr1.chrUn 333536529 333536529 +hg17.chrX 3639615 3639615 +fr1.chrUn 333536532 333536532 +hg17.chrX 3639622 3639622 +fr1.chrUn 333536539 333536539 +hg17.chrX 3639642 3639642 +fr1.chrUn 333536559 333536559 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