--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pieplot_macs/pieplots_macs.py	Thu Apr 14 11:36:26 2016 -0400
@@ -0,0 +1,127 @@
+'''
+ NAME
+
+ pieplots_macs.py
+
+ SYNOPSIS
+
+python pieplots_macs.py --genefile MACSoutfile_genes.txt --peakfile MACSoutfile_peaks.bed --outfile MACSdirectory/piechart.pdf
+
+
+ DESCRIPTION
+
+Peaks are assigned to the closest gene and then categorized according to their location at different genomic regions (promoter, intron, exon, or after the gene). Sites >10kb away from any gene are considered intergenic. (from Pamela)
+
+'''
+
+__author__='Renan Escalante'
+__email__='renanec@mit.edu'
+
+import pandas as pd
+import matplotlib
+matplotlib.use('pdf')
+from matplotlib import pyplot as plt
+matplotlib.rcParams['pdf.fonttype']=42
+matplotlib.rcParams['font.size']=14
+import sys
+from argparse import ArgumentParser
+
+def map_peaks(gene,peak,outfile,macsFlag):
+    genefile = open(gene, 'r')
+    peakfile = open(peak, 'r')
+
+    types = {'promoter':0, 'after':0, 'intron':0, 'exon': 0}
+
+    #read mapped gene file, store closest map for each peak
+    peaks={} #{chrom:{peakStart:[dist, type]}}
+    for line in genefile:
+        words = line.strip().split('\t')
+        #ignore first line
+        if words[0] == 'knownGeneID': continue
+        chrom = words[2]
+
+
+        if not macsFlag:
+            try:
+                start = int(words[3])
+                dist = abs(int(words[15]))
+                maptype = words[16]
+                if maptype == 'gene':
+                    maptype = words[17]
+            except:
+                pass
+
+        else:
+            start = int(words[3])-1
+            dist = abs(int(words[12]))
+            maptype = words[14]
+            if maptype == 'gene':
+                maptype = words[15]
+
+
+        if chrom not in peaks:
+            #new chrom
+            peaks[chrom] = {start:[dist,maptype]}
+        else:
+            if start in peaks[chrom].keys():
+                #account for duplicate entries - choose closest gene and store type
+                if dist < peaks[chrom][start][0]:
+                    #closer gene
+                    peaks[chrom][start] = [dist, maptype]
+            else: peaks[chrom][start] = [dist, maptype]
+
+    #count types - 1 per peak in peak file
+    types = {'promoter':0, 'after':0, 'intron':0, 'exon': 0, 'inter': 0}
+    totalpks = 0
+    #Read peak file in bed format
+    for line in peakfile:
+        words = line.strip().split('\t')
+        chrom = words[0]
+        start = int(words[1])
+        if chrom in peaks:
+            if start in peaks[chrom]:
+                types[peaks[chrom][start][1]] += 1
+            else:
+                types['inter'] += 1
+        else:
+            types['inter'] += 1
+        totalpks += 1
+
+
+    #--------------------------------------------
+    #  make a square figure and axes
+    #--------------------------------------------
+
+    fig = plt.figure(figsize=(6,6))
+    pie_ax = fig.add_axes((0.3,0.2,0.4,0.4))
+
+    # The slices will be ordered and plotted counter-clockwise.
+    labels = ['exon: %i'%types['exon'],'intron: %i'%types['intron'],'promoter: %i'%types['promoter'],'intergenic: %i'%types['inter'], 'after: %i'%types['after']]
+    fracs = [types['exon'], types['intron'], types['promoter'], types['inter'], types['after']]
+
+    plt.pie(fracs, labels=labels) #, autopct='%1.1f%%')
+
+    #Export data frame with all the counts
+    indexDataFrame = ['exon','intron','promoter','intergenic','after']
+    df = pd.DataFrame(data=fracs, index=indexDataFrame)
+    dfFileName = outfile.replace("pdf","csv")
+    df.to_csv(dfFileName, sep=',')
+    #plt.title('MACS peaks in %s'%(name))
+    plt.figtext(.5, .1, 'Total: %i'%totalpks, ha='center')
+    fig.savefig(outfile)
+
+def main():
+    usage = "usage: %prog --genefile MACSoutfile_genes.txt --peakfile MACSoutfile_peaks.bed --outfile MACSdirectory/piechart.pdf"
+    parser = ArgumentParser(usage)
+    parser.add_argument("--genefile", dest="genefile", help="Path to file MACS_mfold10,30_pval1e-5_genes.txt")
+    parser.add_argument("--peakfile", dest="peakfile", help="Path to file MACS_mfold10,30_pval1e-5_peaks.bed")
+    parser.add_argument("--outfile", dest="outfile", default="MACS_piechart.pdf", help="Path to pdf file where you want to store the piechart")
+    parser.add_argument('--MACS',action='store_true',default=False,help='Set this value if you have MACS peaks')
+
+    args=parser.parse_args()
+
+    map_peaks(args.genefile, args.peakfile, args.outfile, args.MACS)
+
+
+if __name__=='__main__':
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pieplot_macs/pieplots_macs.xml	Thu Apr 14 11:36:26 2016 -0400
@@ -0,0 +1,22 @@
+<tool id="pieplots_macs" name="Pieplots MACS" version="0.1">
+  <description>
+    Peaks are assigned to the closest gene and then categorized according to their location at different genomic regions (promoter, intron, exon, or after the gene). Sites >10kb away from any gene are considered intergenic.
+  </description>
+  <parallelism method="basic"></parallelism>
+  <requirements>
+    <requirement type="package" version="0.14.1">pandas</requirement>
+    <requirement type="package" version="1.4">matplotlib</requirement>
+  </requirements>
+  <command interpreter="python">
+    pieplots_macs.py --genefile $genefile --peakfile $peakfile $MACS --outfile $out
+  </command>
+  <inputs>
+    <param name="genefile" type="data" label="Gene file (map_peaks_to_genes)" help="" optional="false" />
+    <param name="peakfile" type="data" label="Peaks file (narrowpeaks)" help="" optional="false" />
+    <param name="MACS" checked="false" label="Set this value if you have MACS peaks" type="boolean" truevalue="--MACS" falsevalue="" help="" />
+  </inputs>
+  <outputs>
+    <data name="out" format="pdf" hidden="false" />
+  </outputs>
+  <help></help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pieplot_macs/tool_dependencies.xml	Thu Apr 14 11:36:26 2016 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="pandas" version="0.14.1">
+        <repository changeset_revision="ac9f317487a9" name="package_pandas_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu/" />
+    </package>
+</tool_dependency>