--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chipsequtil/map_to_known_genes.py	Mon Mar 28 13:08:59 2016 -0400
@@ -0,0 +1,236 @@
+#!/usr/local/bin/python
+
+import sys, os
+from optparse import OptionParser
+from collections import defaultdict as dd
+from csv import DictReader, DictWriter
+
+from chipsequtil import MACSFile, BEDFile, KnownGeneFile, parse_number
+from chipsequtil.util import MultiLineHelpFormatter
+
+usage = '%prog [options] <knownGene file> <knownGene xRef file> <peaks file>'
+description = """
+Map the peaks in <peaks file> to genes in <knownGene file>.  <knownGene file> is\
+format is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.\
+<peaks file> format is as produced by MACS.  If *auto* is chosen (default) file extension \
+is examined for *.xls* for default MACS format or *.bed* for BED format.  If the --detail \
+option is provided, the following extra fields are appended to each row:
+
+peak loc, dist from feature, map type, map subtype
+"""
+epilog = ''
+parser = OptionParser(usage=usage,description=description,epilog=epilog,formatter=MultiLineHelpFormatter())
+parser.add_option('--upstream-window',dest='upst_win',type='int',default=5500,help='window width in base pairs to consider promoter region [default: %default]')
+parser.add_option('--downstream-window',dest='dnst_win',type='int',default=2500,help='window width in base pairs to consider downstream region [default: %default]')
+parser.add_option('--tss',dest='tss',action='store_true',help='calculate downstream window from transcription start site instead of transcription end site')
+parser.add_option('--map-output',dest='peak_output',default=None,help='filename to output mapped peaks to [default: stdout]')
+parser.add_option('--stats-output',dest='stats_output',default=sys.stderr,help='filename to output summary stats in conversion [default: stderr]')
+parser.add_option('--peaks-format',dest='peaks_fmt',default='auto',type='choice',choices=['auto','MACS','BED'],help='format of peaks input file [default: %default]')
+parser.add_option('--detail',dest='detail',action='store_true',help='add extra fields to output, see description')
+parser.add_option('--intergenic',dest='intergenic',action='store_true',help='write intergenic peaks to the gene file as well with None as gene ID')
+#parser.add_option('--symbol-xref',dest='symbol_xref',default=None,help='use the kgXref table file supplied to find a gene symbol, output as second column')
+
+# TODO - options
+#parser.add_option('--use-cds',dest='use_cds',action='store_true',help='use cdsStart and cdsEnd fields instead of txStart and txEnd to do mapping')
+#parser.add_option('--capture-intergenic'...)
+#parser.add_option('--map-format',dest='peak_format',type='choice',choices=['default','BED'],help='format of peak output [default: %default]')
+#parser.add_option('--stats-format',dest='stats_format',type='choice',choices=['human','python'],help='format of summary stats output [default: %default]')
+
+def parse_gene_ref(ref_gene) :
+    reader = KnownGeneFile(ref_gene)
+    gene_ref = dd(list)
+    for ref_dict in reader :
+        gene_ref[ref_dict['chrom']].append(ref_dict)
+
+    return gene_ref
+
+def parse_gene_ref_line(l) :
+    l = map(parse_number, l) # coerce to numbers where possible
+    l[9] = map(parse_number, l[9].split(',')) # turn 'x,x,x,...' into list
+    l[10] = map(parse_number, l[10].split(','))
+    return l
+
+if __name__ == '__main__' :
+
+    opts, args = parser.parse_args(sys.argv[1:])
+
+    if len(args) < 3 :
+        parser.error('Must provide three filename arguments')
+
+    gene_ref = parse_gene_ref(args[0])
+    xref_fn = args[1]
+    peaks_fn = args[2]
+    if opts.peaks_fmt == 'auto' :
+        path,ext = os.path.splitext(peaks_fn)
+        if ext.lower() == '.xls' :
+            opts.peaks_fmt = 'MACS'
+        elif ext.lower() == '.bed' :
+            opts.peaks_fmt = 'BED'
+        elif ext.lower() == '.narrowpeak' :
+            opts.peaks_fmt = 'BED'
+        else :
+            parser.error('Could not guess peaks file format by extension (%s), aborting'%ext)
+
+    if opts.peaks_fmt == 'MACS' :
+        peaks_reader_cls = MACSFile
+        chr_field, start_field, end_field = 'chr', 'start', 'end'
+    elif opts.peaks_fmt == 'BED' :
+        peaks_reader_cls = BEDFile
+        chr_field, start_field, end_field = 'chrom', 'chromStart', 'chromEnd'
+    else :
+        # should never happen
+        fieldnames = []
+
+    #peaks_reader = DictReader(open(args[1]),fieldnames=fieldnames,delimiter='\t')
+    peaks_reader = peaks_reader_cls(peaks_fn)
+
+    # default output format:
+    if opts.peak_output :
+        peak_output = open(opts.peak_output,'w')
+    else :
+        peak_output = sys.stdout
+
+    fieldnames = peaks_reader.FIELD_NAMES
+    if opts.detail :
+        fieldnames += ["peak loc","dist from feature","map type","map subtype"]#"score"
+    output_fields = ['knownGeneID']+fieldnames
+
+    # see if the user wants gene symbols too
+    # TODO - actually make this an option, or make it required
+    opts.symbol_xref = xref_fn
+    if opts.symbol_xref :
+        kgXref_fieldnames = ['kgID','mRNA','spID','spDisplayID','geneSymbol','refseq','protAcc','description']
+        symbol_xref_reader = DictReader(open(opts.symbol_xref),fieldnames=kgXref_fieldnames,delimiter='\t')
+        symbol_xref_map = {}
+        for rec in symbol_xref_reader :
+            symbol_xref_map[rec['kgID']] = rec
+        output_fields = ['knownGeneID','geneSymbol']+fieldnames
+
+    peaks_writer = DictWriter(peak_output,output_fields,delimiter='\t',extrasaction='ignore',lineterminator='\n')
+    peaks_writer.writerow(dict([(k,k) for k in output_fields]))
+    unique_genes = set()
+    map_stats = dd(int)
+    for peak in peaks_reader :
+
+        # if this is a comment or header line get skip it
+        if peak[fieldnames[0]].startswith('#') or \
+           peak[fieldnames[0]] == fieldnames[0] or \
+           peak[fieldnames[0]].startswith('track') : continue
+
+        # coerce values to numeric if possible
+        for k,v in peak.items() : peak[k] = parse_number(v)
+
+        # MACS output gives us summit
+        if opts.peaks_fmt == 'MACS' :
+            peak_loc = peak[start_field]+peak['summit']
+        else : # peak assumed to be in the middle of the reported peak range
+            peak_loc = (peak[start_field]+peak[end_field])/2
+
+        chrom_genes = gene_ref[peak[chr_field]]
+
+        if len(chrom_genes) == 0 :
+            sys.stderr.write('WARNING: peak chromosome %s not found in gene reference, skipping: %s\n'%(peak[chr_field],peak))
+            continue
+
+        mapped = False
+
+        # walk through the genes for this chromosome
+        for gene in chrom_genes :
+
+            # reusable dictionary for output
+            out_d = {}.fromkeys(output_fields,0)
+            out_d.update(peak)
+            out_d['map type'] = ''
+            out_d['chromo'] = peak[chr_field]
+            out_d['peak loc'] = peak_loc
+
+            # determine intervals for promoter, gene, and downstream
+            if gene['strand'] == '+' :
+                promoter_coords = max(gene['txStart']-1-opts.upst_win,0), gene['txStart']-1
+                if opts.tss :
+                    gene_coords = gene['txStart'], min(gene['txEnd'],gene['txStart']+opts.dnst_win)
+                    downstream_coords = gene['txEnd']+1,gene['txStart']+opts.dnst_win
+                else :
+                    gene_coords = gene['txStart'], gene['txEnd']
+                    downstream_coords = gene['txEnd']+1, gene['txEnd']+1+opts.dnst_win
+            else :
+                promoter_coords = gene['txEnd']+1, gene['txEnd']+1+opts.upst_win # +1 because we're using 1 based indexing
+                if opts.tss :
+                    gene_coords = max(gene['txStart'],gene['txEnd']-opts.upst_win), gene['txEnd']
+                    downstream_coords = gene['txEnd']-1-opts.dnst_win, gene['txStart']-1 # -1 because we're using 1 based indexing
+                else :
+                    gene_coords = gene['txStart'], gene['txEnd']
+                    downstream_coords = gene['txStart']-1-opts.dnst_win, gene['txStart']-1 # -1 because we're using 1 based indexing
+
+            # check for promoter
+            if peak_loc >= promoter_coords[0] and peak_loc <= promoter_coords[1] :
+                out_d['map type'] = 'promoter'
+                out_d['dist from feature'] = peak_loc - promoter_coords[1] if gene['strand'] == '+' else promoter_coords[0] - peak_loc
+
+            # check for gene
+            elif peak_loc >= gene_coords[0] and peak_loc <= gene_coords[1] :
+                # check for intron/exon
+                exon_coords = zip(gene['exonStarts'],gene['exonEnds'])
+                in_exon = False
+                for st,en in exon_coords :
+                    if peak_loc >= st and peak_loc <= en :
+                        in_exon = True
+                        break
+                out_d['map type'] = 'gene'
+                out_d['map subtype'] = 'exon' if in_exon else 'intron'
+
+                #Commented out to keep score reported in bed file - AJD 7/29/14
+                # score = (peak-TSS)/(TSE-TSS) - peak distance from TSS as fraction of length of gene
+                #gene_len = float(gene_coords[1]-gene_coords[0])
+                #out_d['score'] = (peak_loc-gene_coords[0])/gene_len if gene['strand'] == '+' else (gene_coords[1]-peak_loc)/gene_len
+
+                # distance calculated from start of gene
+                out_d['dist from feature'] = peak_loc - promoter_coords[1] if gene['strand'] == '+' else promoter_coords[0] - peak_loc
+
+                map_stats[out_d['map subtype']] += 1
+
+            # check for downstream
+            elif peak_loc >= downstream_coords[0] and peak_loc <= downstream_coords[1] :
+                out_d['map type'] = 'after'
+                if opts.tss :
+                    out_d['dist from feature'] = peak_loc - gene_coords[0] if gene['strand'] == '+' else gene_coords[1] - peak_loc
+                else :
+                    out_d['dist from feature'] = peak_loc - downstream_coords[0] if gene['strand'] == '+' else downstream_coords[1] - peak_loc
+
+            # does not map to this gene
+            else :
+                pass
+
+            # map type is not blank if we mapped to something
+            if out_d['map type'] != '' :
+
+                #out_d = {'knownGeneID':gene['name']}
+                out_d['knownGeneID'] = gene['name']
+                if opts.symbol_xref :
+                    out_d['geneSymbol'] = symbol_xref_map[gene['name']]['geneSymbol']
+                peaks_writer.writerow(out_d)
+
+                mapped = True
+
+                # reset map_type
+                out_d['map type'] = ''
+
+        if not mapped :
+            if opts.intergenic :
+                out_d['knownGeneID'] = 'None'
+                out_d['geneSymbol'] = 'None'
+                out_d['map type'] = 'intergenic'
+                peaks_writer.writerow(out_d)
+            map_stats['intergenic'] += 1
+
+    if peak_output != sys.stdout :
+        peak_output.close()
+
+    #if opts.stats_output != sys.stderr :
+    #    opts.stats_output = open(opts.stats_output,'w')
+
+    #for k,v in map_stats.items() :
+    #    opts.stats_output.write('%s: %s\n'%(k,v))
+
+    #if opts.stats_output != sys.stderr :
+    #    opts.stats_output.close()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chipsequtil/map_to_known_genes.xml	Mon Mar 28 13:08:59 2016 -0400
@@ -0,0 +1,46 @@
+<tool id="chipsequtil_maptoknowngenes" name="Map Peaks to Known Genes" version="0.1">
+  <description>
+    Map the peaks in &lt;peaks file&gt; to genes in &lt;knownGene file&gt;.  &lt;knownGene file&gt; isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.&lt;peaks file&gt; format is as produced by MACS.  If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format.  If the --detail option is provided, the following extra fields are appended to each row:
+    peak loc, dist from feature, map type, map subtype
+  </description>
+  <parallelism method="basic"></parallelism>
+  <requirements>
+    <requirement type="package" version="1.0">chipsequtil</requirement>
+  </requirements>
+  <command interpreter="python">
+    map_to_known_genes.py
+      $tss
+      --upstream-window=$upst_win
+      --downstream-window=$dnst_win
+      --map-output=$peaksOutput
+      --peaks-format=$peaks_fmt
+      $detail
+      $intergenic
+      $knownGeneFile $knownGeneRef $macsPeaksFile
+
+  </command>
+  <inputs>
+    <param name="knownGeneFile" type="data" label="knownGene file" help="" optional="false" />
+    <param name="knownGeneRef" type="data" label="knownGene xRef file" help="" optional="false" />
+    <param name="macsPeaksFile" type="data" label="Peaks File" help="" optional="false" />
+    <param name="peaksOutput" type="text" label="Output filename" help="filename to output mapped peaks to" optional="false" />
+
+    <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" />
+    <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" />
+
+    <param name="tss" checked="true" label="calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" />
+
+    <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false">
+        <option value="auto">auto</option>
+        <option value="MACS">MACS</option>
+        <option selected="true" value="BED">BED</option>
+    </param>
+
+    <param name="detail" checked="false" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" />
+    <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" />
+  </inputs>
+  <outputs>
+    <data format="txt" hidden="false" name="default"/>
+  </outputs>
+  <help></help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chipsequtil/tool_dependencies.xml	Mon Mar 28 13:08:59 2016 -0400
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="chipsequtil" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://github.com/adamlabadorf/chipsequtil/archive/master.zip</action>
+                <action type="shell_command">unzip chipsequtil-master.zip -d chipsequtil</action>
+                <action type="shell_command">cd chipsequtil</action>
+                <action type="shell_command">cp org_settings.cfg src/chipsequtil/</action>
+                <action type="shell_command">python setup.py install</action>
+            </actions>
+        </install>
+        <readme></readme>
+    </package>
+</tool_dependency>