--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WeightedAverage.py	Tue Apr 01 10:48:52 2014 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+"""
+usage: %prog bed_file_1 bed_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file
+    -2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file
+"""
+
+import collections
+import sys
+#import numpy
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+from galaxy.tools.util.galaxyops import *
+from bx.cookbook import doc_optparse
+
+
+#export PYTHONPATH=~/galaxy/lib/
+#running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+
+def FindRate(chromosome, start_stop, dictType):
+    OverlapList = []
+    for tempO in dictType[chromosome]:
+        DatabaseInterval = [tempO[0], tempO[1]]
+        Overlap = GetOverlap( start_stop, DatabaseInterval )
+        if Overlap > 0:
+            OverlapList.append([Overlap, tempO[2]])
+    
+    if len(OverlapList) > 0:
+        SumRecomb = 0
+        SumOverlap = 0
+        for member in OverlapList:
+            SumRecomb += member[0]*member[1]
+            SumOverlap += member[0]
+        averageRate = SumRecomb/SumOverlap
+        return averageRate
+    else:
+        return 'NA'
+
+
+def GetOverlap(a, b):
+    return min(a[1], b[1])-max(a[0], b[0])
+
+
+options, args = doc_optparse.parse( __doc__ )
+
+try:
+    chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 )
+    chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 )
+    input1, input2, input3 = args
+except Exception, eee:
+    print eee
+    stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
+
+fd2 = open(input2)
+lines2 = fd2.readlines()
+RecombChrDict = collections.defaultdict(list)
+
+skipped = 0
+for line in lines2:
+    temp = line.strip().split()
+    try:
+        assert float(temp[int(name_col_2)])
+    except:
+        skipped += 1
+        continue
+    tempIndex = [int(temp[int(start_col_2)]), int(temp[int(end_col_2)]), float(temp[int(name_col_2)])]
+    RecombChrDict[temp[int(chr_col_2)]].append(tempIndex)
+
+print "Skipped %d features with invalid values" % (skipped)
+
+fd1 = open(input1)
+lines = fd1.readlines()
+finalProduct = ''
+for line in lines:
+    temp = line.strip().split('\t')
+    chromosome = temp[int(chr_col_1)]
+    start = int(temp[int(start_col_1)])
+    stop = int(temp[int(end_col_1)])
+    start_stop = [start, stop]
+    RecombRate = FindRate( chromosome, start_stop, RecombChrDict )
+    try:
+        RecombRate = "%.4f" % (float(RecombRate))
+    except:
+        RecombRate = RecombRate
+    finalProduct += line.strip()+'\t'+str(RecombRate)+'\n'
+fdd = open(input3, 'w')
+fdd.writelines(finalProduct)
+fdd.close()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WeightedAverage.xml	Tue Apr 01 10:48:52 2014 -0400
@@ -0,0 +1,71 @@
+<tool id="wtavg" name="Assign weighted-average" version="1.0.0">
+  <description> of the values of features overlapping an interval </description>
+  <command interpreter="python">WeightedAverage.py  $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol}</command>
+
+  <inputs>
+    <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/>
+    <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." />
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="genomic_interval" />
+  </outputs>
+  <tests>
+    <!-- Test data with valid values -->
+    <test>
+      <param name="genomic_interval" value="interval_interpolate.bed"/>
+      <param name="genomic_feature" value="value_interpolate.bed"/>
+      <output name="out_file1" file="interpolate_result.bed"/>
+    </test>
+    
+  </tests>
+  <help>
+
+
+.. class:: infomark
+
+**What it does**
+
+For each interval in your first dataset, this tool calculates the weighted average value of the overlapping features in your second dataset.
+
+- When a genomic interval partially or totally overlaps a single genomic feature, the value of that genomic feature is assigned to the genomic interval.
+- When a genomic interval partially or totally overlaps with more than one genomic features, the average of the values of the overlapping genomic features weighted by the corresponding number of overlapping bases is assigned to the genomic interval.
+- When a genomic interval does not overlap with any genomic feature, 'NA' will be assigned as it's value.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+The input datasets should be in **bed** or **interval** format. Please use "edit attributes"/pencil icon to specify the column containing the values for the features in the second dataset as **name/identifier** column.
+
+The output will contain all the columns in the first input plus a new column containing the assigned value for each interval.
+
+-----
+
+**Example**
+
+- Suppose our first dataset contains the following **genomic intervals**::
+    
+    chr  start stop
+    chr1 1000  2000
+    chr1 3000  5000
+    chr1 8000  9000
+  
+- and our second dataset contains the following **genomic features** each having an associated value (in fourth column) ::
+
+    chr  start stop name
+    chr1 900   1200 0.5
+    chr1 2900  3100 0.2
+    chr1 4800  5100 0.8
+  
+- For each **genomic interval** in our first dataset, this tool calculates the weighted average value of the overlapping **genomic features** in our second dataset ::
+
+    chr1 1000  2000 0.5
+    chr1 3000  5000 0.6
+    chr1 8000  9000 NA
+  
+
+
+</help>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interpolate_result.bed	Tue Apr 01 10:48:52 2014 -0400
@@ -0,0 +1,219 @@
+chr1	27800000	29750669	6600000	0	1.7386
+chr1	29800669	34400000	6600000	0	1.7920
+chr1	46500000	51300000	4800000	0	1.4004
+chr1	102000000	103636494	5000000	0	1.2007
+chr1	103686494	103843838	5000000	0	NA
+chr1	103893838	107000000	5000000	0	1.1883
+chr1	117600000	120498679	3100000	0	1.4007
+chr1	120548679	120700000	3100000	0	NA
+chr1	153300000	154800000	1500000	0	1.9511
+chr1	163800000	171200000	7400000	0	1.4719
+chr1	174300000	184000000	9700000	0	1.5022
+chr10	6700000	12300000	5600000	0	1.5533
+chr10	42100000	45746970	11200000	0	1.4905
+chr10	45896970	46849175	11200000	0	NA
+chr10	46999175	47262482	11200000	0	1.4600
+chr10	47412482	47575713	11200000	0	NA
+chr10	47725713	48715542	11200000	0	1.3900
+chr10	48865542	50807416	11200000	0	1.7448
+chr10	50857416	51068851	11200000	0	NA
+chr10	51118851	53300000	11200000	0	1.3877
+chr10	74600000	81231464	15000000	0	1.4494
+chr10	81241464	89600000	15000000	0	1.4475
+chr10	98000000	99400000	1400000	0	1.7700
+chr10	102000000	111800000	9800000	0	1.4549
+chr10	114900000	119100000	4200000	0	1.3184
+chr10	127400000	128606059	7974737	0	1.2600
+chr10	128656059	133271394	7974737	0	1.3583
+chr10	133281394	133527517	7974737	0	NA
+chr10	133577517	135374737	7974737	0	1.4720
+chr11	50000	1152759	2800000	0	1.5200
+chr11	1169335	2800000	2800000	0	1.6101
+chr11	12600000	16100000	3500000	0	1.2212
+chr11	21600000	26000000	4400000	0	1.3320
+chr11	27200000	31000000	3800000	0	1.2483
+chr11	48800000	50740429	2600000	0	1.3100
+chr11	50947429	51400000	2600000	0	NA
+chr11	56400000	68846377	12800000	0	1.7959
+chr11	68848982	69200000	12800000	0	1.6400
+chr11	70700000	85300000	14600000	0	1.5591
+chr11	87900000	92300000	4400000	0	1.2134
+chr11	110000000	115400000	5400000	0	1.4715
+chr11	120700000	134452384	13752384	0	1.4668
+chr12	36500000	44600000	8100000	0	1.3403
+chr12	53100000	56300000	3200000	0	1.6808
+chr12	69800000	74791940	8900000	0	1.2548
+chr12	75041940	78700000	8900000	0	1.2656
+chr12	91200000	94800000	3600000	0	1.6655
+chr12	100000000	107500000	7500000	0	1.6243
+chr13	18400000	32900000	14500000	0	1.5346
+chr13	34700000	39500000	4800000	0	1.1758
+chr13	52200000	57600000	5400000	0	1.2506
+chr13	60500000	72100000	11600000	0	1.2112
+chr13	100500000	109100000	8600000	0	1.3144
+chr14	23600000	31800000	8200000	0	1.3057
+chr14	36900000	41000000	4100000	0	1.2309
+chr14	43200000	48300000	5100000	0	1.2680
+chr14	69300000	72900000	3600000	0	1.6758
+chr14	78400000	88900000	10500000	0	1.2495
+chr15	23300000	24687593	2400000	0	1.2379
+chr15	24731593	25169606	2400000	0	1.2200
+chr15	25270606	25700000	2400000	0	NA
+chr15	31400000	37900000	6500000	0	1.4543
+chr15	65300000	70400000	5100000	0	1.6950
+chr16	0	8576922	14700000	0	1.5411
+chr16	8594422	14700000	14700000	0	1.5935
+chr16	16700000	21700000	5000000	0	1.6366
+chr16	69400000	78200000	8800000	0	1.4012
+chr16	80500000	82700000	2200000	0	1.5200
+chr17	0	296854	11200000	0	NA
+chr17	343376	11200000	11200000	0	1.7399
+chr17	28800000	31699961	6600000	0	1.4123
+chr17	31799961	33429230	6600000	0	1.7100
+chr17	33529230	35400000	6600000	0	1.8415
+chr17	47600000	54900000	7300000	0	1.4561
+chr17	55600000	59900000	4300000	0	1.5958
+chr18	17300000	31000000	13700000	0	1.3855
+chr18	35500000	50313134	16500000	0	1.3679
+chr18	50360134	52000000	16500000	0	1.3600
+chr19	11000	7297004	12600000	0	1.8232
+chr19	7302004	8593198	12600000	0	2.1300
+chr19	8598198	12600000	12600000	0	1.7010
+chr2	12800000	16171403	4200000	0	1.2641
+chr2	16221403	17000000	4200000	0	1.2505
+chr2	19100000	21012571	4800000	0	1.2500
+chr2	21037571	23900000	4800000	0	1.4405
+chr2	47600000	52700000	5100000	0	1.2384
+chr2	54800000	61100000	6300000	0	1.4715
+chr2	75400000	83700000	8300000	0	1.1639
+chr2	102100000	108600000	6500000	0	1.3381
+chr2	113800000	118600000	4800000	0	1.1949
+chr2	129600000	134800000	5200000	0	1.3332
+chr2	136600000	144700000	8100000	0	1.3447
+chr2	189100000	197100000	8000000	0	1.4590
+chr2	209100000	215100000	6000000	0	1.3963
+chr2	221300000	233711985	15700000	0	1.3701
+chr2	233731985	237000000	15700000	0	1.4560
+chr20	5000000	9000000	4000000	0	1.3515
+chr20	11900000	17800000	5900000	0	1.3648
+chr20	21200000	25700000	4500000	0	1.4588
+chr20	37100000	41100000	4000000	0	1.3980
+chr20	49200000	54400000	5200000	0	1.5272
+chr21	38600000	41877429	8344323	0	1.6542
+chr21	41878628	43505733	8344323	0	1.9800
+chr21	43507092	46944323	8344323	0	1.6567
+chr22	16300000	18889431	11600000	0	NA
+chr22	18939431	27900000	11600000	0	1.6362
+chr22	30500000	39300000	8800000	0	1.7639
+chr22	42600000	43057958	7091432	0	1.5600
+chr22	43107958	47356150	7091432	0	1.5400
+chr22	47366250	48750436	7091432	0	1.4700
+chr22	48767136	49087576	7091432	0	NA
+chr22	49089176	49107103	7091432	0	NA
+chr22	49126803	49591432	7091432	0	NA
+chr3	14700000	23800000	9100000	0	1.3438
+chr3	26400000	32100000	5700000	0	1.2751
+chr3	54400000	58500000	4100000	0	1.4670
+chr3	63700000	66115833	8100000	0	1.1571
+chr3	66375833	71800000	8100000	0	1.4022
+chr3	74200000	87200000	13000000	0	1.2224
+chr3	104400000	123400000	19000000	0	1.4382
+chr3	144400000	150400000	6000000	0	1.2844
+chr4	0	1413146	5200000	0	NA
+chr4	1464146	3883456	5200000	0	1.8696
+chr4	3963456	5200000	5200000	0	1.4193
+chr4	40900000	45600000	4700000	0	1.3101
+chr4	59200000	59429326	17300000	0	NA
+chr4	59479326	69275441	17300000	0	1.1989
+chr4	69375441	71536854	17300000	0	1.4800
+chr4	71711854	75641303	17300000	0	1.3813
+chr4	75671303	76500000	17300000	0	NA
+chr4	102500000	120600000	18100000	0	1.2796
+chr4	124000000	151000000	27000000	0	1.3180
+chr5	42400000	45800000	3400000	0	1.6600
+chr5	135400000	138812257	11800000	0	1.6903
+chr5	138817257	147200000	11800000	0	1.4559
+chr6	5000	4100000	4100000	0	1.4960
+chr6	7000000	9199728	6500000	0	1.3742
+chr6	9249728	13500000	6500000	0	1.5531
+chr6	15500000	23500000	8000000	0	1.3678
+chr6	26100000	40600000	14500000	0	1.5998
+chr6	45200000	57200000	12000000	0	1.3561
+chr6	63500000	70000000	6500000	0	1.2305
+chr6	75900000	87500000	11600000	0	1.3037
+chr6	92100000	95737264	7800000	0	1.1620
+chr6	95937264	99900000	7800000	0	1.2897
+chr6	139100000	149100000	10000000	0	1.4172
+chr6	164400000	167766922	6499992	0	1.2400
+chr6	167784922	170021897	6499992	0	1.5383
+chr6	170171897	170896992	6499992	0	1.4900
+chr7	19500000	35600000	16100000	0	1.5139
+chr7	37500000	43300000	5800000	0	1.4283
+chr7	46600000	48167949	7300000	0	1.3900
+chr7	48207949	50338125	7300000	0	1.4468
+chr7	50378125	53900000	7300000	0	1.3027
+chr7	61100000	61314455	36800000	0	NA
+chr7	61364455	61554592	36800000	0	NA
+chr7	61604592	74353660	36800000	0	1.4805
+chr7	74603660	97900000	36800000	0	1.3240
+chr7	117200000	130100000	12900000	0	1.3323
+chr7	132400000	137300000	4900000	0	1.4019
+chr7	142800000	147500000	4700000	0	1.1759
+chr8	12700000	19100000	6400000	0	1.1690
+chr8	29700000	29732668	8800000	0	NA
+chr8	29798768	38500000	8800000	0	1.4250
+chr8	55600000	66100000	10500000	0	1.5225
+chr8	74000000	86069241	13200000	0	1.3023
+chr8	86193341	86763703	13200000	0	NA
+chr8	86851003	87200000	13200000	0	NA
+chr8	99100000	101600000	2500000	0	1.6452
+chr8	106100000	117700000	11600000	0	1.2240
+chr8	127300000	140000000	12700000	0	1.4038
+chr9	9000000	14100000	5100000	0	1.2167
+chr9	40200000	40223029	6500000	0	NA
+chr9	40273029	40415834	6500000	0	NA
+chr9	40465834	40930341	6500000	0	NA
+chr9	40980341	41133214	6500000	0	NA
+chr9	41183214	41355793	6500000	0	NA
+chr9	41405793	42603951	6500000	0	NA
+chr9	42653951	43203694	6500000	0	NA
+chr9	43253694	43886565	6500000	0	NA
+chr9	43936565	44616642	6500000	0	NA
+chr9	44666642	44848289	6500000	0	NA
+chr9	44898289	45190199	6500000	0	NA
+chr9	45240199	45705517	6500000	0	NA
+chr9	45755517	46106426	6500000	0	NA
+chr9	46156426	46351035	6500000	0	NA
+chr9	46401035	46700000	6500000	0	NA
+chr9	91000000	91533236	10600000	0	NA
+chr9	91583236	91668616	10600000	0	NA
+chr9	91718616	101600000	10600000	0	1.5580
+chrX	0	34821	6000000	0	NA
+chrX	84821	171384	6000000	0	NA
+chrX	201384	967557	6000000	0	NA
+chrX	1017557	1054113	6000000	0	NA
+chrX	1104113	1184234	6000000	0	NA
+chrX	1274234	2028238	6000000	0	NA
+chrX	2128238	6000000	6000000	0	1.4520
+chrX	9500000	37008177	37800000	0	1.4047
+chrX	37033177	47300000	37800000	0	1.4817
+chrX	65000000	67700000	2700000	0	1.2658
+chrX	76000000	76570348	22200000	0	NA
+chrX	76590348	98200000	22200000	0	1.2642
+chrX	102500000	113403924	18200000	0	1.3809
+chrX	113473924	115596318	18200000	0	1.3900
+chrX	115616318	120700000	18200000	0	1.4886
+chrX	137800000	140100000	2300000	0	1.2054
+chrX	141900000	143335010	5000000	0	1.2700
+chrX	143365010	146900000	5000000	0	1.2517
+chrY	0	34821	11200000	0	NA
+chrY	84821	171384	11200000	0	NA
+chrY	201384	967557	11200000	0	NA
+chrY	1017557	1054113	11200000	0	NA
+chrY	1104113	1184234	11200000	0	NA
+chrY	1274234	2028238	11200000	0	NA
+chrY	2128238	8974955	11200000	0	1.3987
+chrY	9024955	9301322	11200000	0	NA
+chrY	9901322	10714553	11200000	0	1.2200
+chrY	12500000	22310816	14700000	0	1.3632
+chrY	22360816	27200000	14700000	0	1.2357
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interval_interpolate.bed	Tue Apr 01 10:48:52 2014 -0400
@@ -0,0 +1,219 @@
+chr1	27800000	29750669	6600000	0
+chr1	29800669	34400000	6600000	0
+chr1	46500000	51300000	4800000	0
+chr1	102000000	103636494	5000000	0
+chr1	103686494	103843838	5000000	0
+chr1	103893838	107000000	5000000	0
+chr1	117600000	120498679	3100000	0
+chr1	120548679	120700000	3100000	0
+chr1	153300000	154800000	1500000	0
+chr1	163800000	171200000	7400000	0
+chr1	174300000	184000000	9700000	0
+chr10	6700000	12300000	5600000	0
+chr10	42100000	45746970	11200000	0
+chr10	45896970	46849175	11200000	0
+chr10	46999175	47262482	11200000	0
+chr10	47412482	47575713	11200000	0
+chr10	47725713	48715542	11200000	0
+chr10	48865542	50807416	11200000	0
+chr10	50857416	51068851	11200000	0
+chr10	51118851	53300000	11200000	0
+chr10	74600000	81231464	15000000	0
+chr10	81241464	89600000	15000000	0
+chr10	98000000	99400000	1400000	0
+chr10	102000000	111800000	9800000	0
+chr10	114900000	119100000	4200000	0
+chr10	127400000	128606059	7974737	0
+chr10	128656059	133271394	7974737	0
+chr10	133281394	133527517	7974737	0
+chr10	133577517	135374737	7974737	0
+chr11	50000	1152759	2800000	0
+chr11	1169335	2800000	2800000	0
+chr11	12600000	16100000	3500000	0
+chr11	21600000	26000000	4400000	0
+chr11	27200000	31000000	3800000	0
+chr11	48800000	50740429	2600000	0
+chr11	50947429	51400000	2600000	0
+chr11	56400000	68846377	12800000	0
+chr11	68848982	69200000	12800000	0
+chr11	70700000	85300000	14600000	0
+chr11	87900000	92300000	4400000	0
+chr11	110000000	115400000	5400000	0
+chr11	120700000	134452384	13752384	0
+chr12	36500000	44600000	8100000	0
+chr12	53100000	56300000	3200000	0
+chr12	69800000	74791940	8900000	0
+chr12	75041940	78700000	8900000	0
+chr12	91200000	94800000	3600000	0
+chr12	100000000	107500000	7500000	0
+chr13	18400000	32900000	14500000	0
+chr13	34700000	39500000	4800000	0
+chr13	52200000	57600000	5400000	0
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/value_interpolate.bed	Tue Apr 01 10:48:52 2014 -0400
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\ No newline at end of file