Mercurial > repos > artbio > small_rna_maps
changeset 25:07aa8f928d4b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit a4aa17f675a9caaca0859fee210fae6ada74460f
| author | artbio |
|---|---|
| date | Wed, 10 Apr 2019 06:38:33 -0400 |
| parents | e75a10eba0a6 |
| children | 376fae7c9f32 |
| files | small_rna_maps.py small_rna_maps.xml test-data/input1_input2_size.tab test-data/input1_min20_max30_size.tab test-data/size.tab |
| diffstat | 5 files changed, 2384 insertions(+), 2359 deletions(-) [+] |
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--- a/small_rna_maps.py Sun Mar 31 20:58:21 2019 -0400 +++ b/small_rna_maps.py Wed Apr 10 06:38:33 2019 -0400 @@ -290,18 +290,42 @@ ''' Writer of a tabular file Dataset, Chromosome, Chrom_length, <category (size)>, <some value> + from a dictionary of sizes: {chrom: {polarity: {size: nbre of reads}}} out is an *open* file handler ''' for chrom in sorted(sizedic): sizes = sizedic[chrom]['F'].keys() sizes.extend(sizedic[chrom]['R'].keys()) + strandness = defaultdict(int) + sizeness = defaultdict(int) + for polarity in sizedic[chrom]: + for size in range(min(sizes), max(sizes)+1): + try: + strandness[polarity] += sizedic[chrom][polarity][size] + except KeyError: + pass + sizeness[size] += sizedic[chrom][polarity][size] + Strandbias = strandness['F'] + strandness['R'] + if Strandbias: + Strandbias = strandness['F'] / float(Strandbias) + else: + Strandbias = 2 + Mean = numpy.mean(sizeness.values()) + StDev = numpy.std(sizeness.values()) + for size in sizeness: + if StDev: + sizeness[size] = (sizeness[size] - Mean) / StDev + else: + sizeness[size] = 0 for polarity in sorted(sizedic[chrom]): for size in range(min(sizes), max(sizes)+1): try: line = [self.sample_name, chrom, polarity, size, - sizedic[chrom][polarity][size]] + sizedic[chrom][polarity][size], + Strandbias, sizeness[size]] except KeyError: - line = [self.sample_name, chrom, polarity, size, 0] + line = [self.sample_name, chrom, polarity, size, 0, + Strandbias, sizeness[size]] line = [str(i) for i in line] out.write('\t'.join(line) + '\n') @@ -355,7 +379,8 @@ for method, output in zip(methods, outputs): out = open(output, 'w') if method == 'Size': - header = ["Dataset", "Chromosome", "Polarity", method, "Counts"] + header = ["Dataset", "Chromosome", "Polarity", method, "Counts", + "Strandness", "z-score"] elif cluster: header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate", "Polarity", method, "Start-End", "Cluster Size",
--- a/small_rna_maps.xml Sun Mar 31 20:58:21 2019 -0400 +++ b/small_rna_maps.xml Wed Apr 10 06:38:33 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="2.12.0"> +<tool id="small_rna_maps" name="small_rna_maps" version="2.13.0"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
--- a/test-data/input1_input2_size.tab Sun Mar 31 20:58:21 2019 -0400 +++ b/test-data/input1_input2_size.tab Wed Apr 10 06:38:33 2019 -0400 @@ -1,1045 +1,1045 @@ -Dataset Chromosome Polarity Size Counts -input1.bam FBtr0070001 F 16 2 -input1.bam FBtr0070001 F 17 1 -input1.bam FBtr0070001 F 18 0 -input1.bam FBtr0070001 F 19 1 -input1.bam FBtr0070001 F 20 4 -input1.bam FBtr0070001 F 21 4 -input1.bam FBtr0070001 F 22 29 -input1.bam FBtr0070001 F 23 15 -input1.bam FBtr0070001 F 24 1 -input1.bam FBtr0070001 R 16 0 -input1.bam FBtr0070001 R 17 0 -input1.bam FBtr0070001 R 18 0 -input1.bam FBtr0070001 R 19 0 -input1.bam FBtr0070001 R 20 0 -input1.bam FBtr0070001 R 21 0 -input1.bam FBtr0070001 R 22 0 -input1.bam FBtr0070001 R 23 0 -input1.bam FBtr0070001 R 24 0 -input1.bam FBtr0070533 F 15 2 -input1.bam FBtr0070533 F 16 1 -input1.bam FBtr0070533 F 17 1 -input1.bam FBtr0070533 F 18 6 -input1.bam FBtr0070533 F 19 3 -input1.bam FBtr0070533 F 20 2 -input1.bam FBtr0070533 F 21 2 -input1.bam 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FBtr0079596 F 24 1 0.996835443038 -1.36189789133 +input2.bam FBtr0079596 R 15 0 0.996835443038 -0.0267038802222 +input2.bam FBtr0079596 R 16 0 0.996835443038 -0.471768550592 +input2.bam FBtr0079596 R 17 0 0.996835443038 -0.605287951703 +input2.bam FBtr0079596 R 18 0 0.996835443038 2.10960653755 +input2.bam FBtr0079596 R 19 0 0.996835443038 0.729906059406 +input2.bam FBtr0079596 R 20 0 0.996835443038 0.774412526443 +input2.bam FBtr0079596 R 21 1 0.996835443038 0.418360790148 +input2.bam FBtr0079596 R 22 0 0.996835443038 -0.249236215407 +input2.bam FBtr0079596 R 23 0 0.996835443038 -1.31739142429 +input2.bam FBtr0079596 R 24 0 0.996835443038 -1.36189789133 +input2.bam FBtr0079677 F 15 2 1.0 1.21267812518 +input2.bam FBtr0079677 F 16 1 1.0 -0.242535625036 +input2.bam FBtr0079677 F 17 2 1.0 1.21267812518 +input2.bam FBtr0079677 F 18 0 1.0 -1.69774937525 +input2.bam FBtr0079677 F 19 1 1.0 -0.242535625036 +input2.bam FBtr0079677 F 20 1 1.0 -0.242535625036 +input2.bam FBtr0079677 R 15 0 1.0 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R 17 0 1.0 0.0 +input2.bam FBtr0079702 R 18 0 1.0 0.0 +input2.bam FBtr0079728 F 15 3 1.0 1.73205080757 +input2.bam FBtr0079728 F 16 1 1.0 -0.57735026919 +input2.bam FBtr0079728 F 17 1 1.0 -0.57735026919 +input2.bam FBtr0079728 F 18 1 1.0 -0.57735026919 +input2.bam FBtr0079728 R 15 0 1.0 1.73205080757 +input2.bam FBtr0079728 R 16 0 1.0 -0.57735026919 +input2.bam FBtr0079728 R 17 0 1.0 -0.57735026919 +input2.bam FBtr0079728 R 18 0 1.0 -0.57735026919 +input2.bam FBtr0079729 F 15 1 1.0 -0.707106781187 +input2.bam FBtr0079729 F 16 2 1.0 1.41421356237 +input2.bam FBtr0079729 F 17 1 1.0 -0.707106781187 +input2.bam FBtr0079729 R 15 0 1.0 -0.707106781187 +input2.bam FBtr0079729 R 16 0 1.0 1.41421356237 +input2.bam FBtr0079729 R 17 0 1.0 -0.707106781187 +input2.bam FBtr0079752 F 17 1 1.0 1.73205080757 +input2.bam FBtr0079752 F 18 0 1.0 -0.57735026919 +input2.bam FBtr0079752 F 19 0 1.0 -0.57735026919 +input2.bam FBtr0079752 F 20 0 1.0 -0.57735026919 +input2.bam FBtr0079752 F 21 0 1.0 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1.42187198314 +input2.bam FBtr0079820 R 16 0 1.0 -0.385367173 +input2.bam FBtr0079820 R 17 0 1.0 -0.704291729965 +input2.bam FBtr0079820 R 18 0 1.0 -0.59798354431 +input2.bam FBtr0079820 R 19 0 1.0 1.20925561183 +input2.bam FBtr0079820 R 20 0 1.0 1.10294742617 +input2.bam FBtr0079820 R 21 0 1.0 -0.704291729965 +input2.bam FBtr0079820 R 22 0 1.0 -1.3421408439 +input2.bam FBtr0080609 F 17 2 1.0 1.50755672289 +input2.bam FBtr0080609 F 18 1 1.0 0.150755672289 +input2.bam FBtr0080609 F 19 2 1.0 1.50755672289 +input2.bam FBtr0080609 F 20 0 1.0 -1.20604537831 +input2.bam FBtr0080609 F 21 0 1.0 -1.20604537831 +input2.bam FBtr0080609 F 22 1 1.0 0.150755672289 +input2.bam FBtr0080609 F 23 1 1.0 0.150755672289 +input2.bam FBtr0080609 F 24 0 1.0 -1.20604537831 +input2.bam FBtr0080609 F 25 1 1.0 0.150755672289 +input2.bam FBtr0080609 R 17 0 1.0 1.50755672289 +input2.bam FBtr0080609 R 18 0 1.0 0.150755672289 +input2.bam FBtr0080609 R 19 0 1.0 1.50755672289 +input2.bam FBtr0080609 R 20 0 1.0 -1.20604537831 +input2.bam FBtr0080609 R 21 0 1.0 -1.20604537831 +input2.bam FBtr0080609 R 22 0 1.0 0.150755672289 +input2.bam FBtr0080609 R 23 0 1.0 0.150755672289 +input2.bam FBtr0080609 R 24 0 1.0 -1.20604537831 +input2.bam FBtr0080609 R 25 0 1.0 0.150755672289 +input2.bam FBtr0080644 F 15 8 1.0 0 +input2.bam FBtr0080644 R 15 0 1.0 0 +input2.bam FBtr0080646 F 15 10 1.0 2.42935266809 +input2.bam FBtr0080646 F 16 1 1.0 -0.209426954146 +input2.bam FBtr0080646 F 17 0 1.0 -0.50262468995 +input2.bam FBtr0080646 F 18 0 1.0 -0.50262468995 +input2.bam FBtr0080646 F 19 0 1.0 -0.50262468995 +input2.bam FBtr0080646 F 20 0 1.0 -0.50262468995 +input2.bam FBtr0080646 F 21 1 1.0 -0.209426954146 +input2.bam FBtr0080646 R 15 0 1.0 2.42935266809 +input2.bam FBtr0080646 R 16 0 1.0 -0.209426954146 +input2.bam FBtr0080646 R 17 0 1.0 -0.50262468995 +input2.bam FBtr0080646 R 18 0 1.0 -0.50262468995 +input2.bam FBtr0080646 R 19 0 1.0 -0.50262468995 +input2.bam FBtr0080646 R 20 0 1.0 -0.50262468995 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FBtr0080663 F 24 1 1.0 -1.0784474791 +input2.bam FBtr0080663 R 15 0 1.0 1.73000949772 +input2.bam FBtr0080663 R 16 0 1.0 0.381950148847 +input2.bam FBtr0080663 R 17 0 1.0 0.381950148847 +input2.bam FBtr0080663 R 18 0 1.0 1.73000949772 +input2.bam FBtr0080663 R 19 0 1.0 -0.179741246516 +input2.bam FBtr0080663 R 20 0 1.0 -0.404417804661 +input2.bam FBtr0080663 R 21 0 1.0 -0.741432641879 +input2.bam FBtr0080663 R 22 0 1.0 -0.629094362806 +input2.bam FBtr0080663 R 23 0 1.0 -1.19078575817 +input2.bam FBtr0080663 R 24 0 1.0 -1.0784474791 +input2.bam FBtr0080664 F 15 165 0.994858611825 2.88880021869 +input2.bam FBtr0080664 F 16 59 0.994858611825 0.579212614557 +input2.bam FBtr0080664 F 17 20 0.994858611825 -0.270541315264 +input2.bam FBtr0080664 F 18 75 0.994858611825 0.927829611407 +input2.bam FBtr0080664 F 19 24 0.994858611825 -0.183387066051 +input2.bam FBtr0080664 F 20 21 0.994858611825 -0.24875275296 +input2.bam FBtr0080664 F 21 8 0.994858611825 -0.532004062901 +input2.bam FBtr0080664 F 22 4 0.994858611825 -0.59736974981 +input2.bam FBtr0080664 F 23 4 0.994858611825 -0.59736974981 +input2.bam FBtr0080664 F 24 0 0.994858611825 -0.706312561326 +input2.bam FBtr0080664 F 25 3 0.994858611825 -0.640946874416 +input2.bam FBtr0080664 F 26 4 0.994858611825 -0.619158312113 +input2.bam FBtr0080664 R 15 0 0.994858611825 2.88880021869 +input2.bam FBtr0080664 R 16 0 0.994858611825 0.579212614557 +input2.bam FBtr0080664 R 17 0 0.994858611825 -0.270541315264 +input2.bam FBtr0080664 R 18 0 0.994858611825 0.927829611407 +input2.bam FBtr0080664 R 19 0 0.994858611825 -0.183387066051 +input2.bam FBtr0080664 R 20 0 0.994858611825 -0.24875275296 +input2.bam FBtr0080664 R 21 0 0.994858611825 -0.532004062901 +input2.bam FBtr0080664 R 22 1 0.994858611825 -0.59736974981 +input2.bam FBtr0080664 R 23 1 0.994858611825 -0.59736974981 +input2.bam FBtr0080664 R 24 0 0.994858611825 -0.706312561326 +input2.bam FBtr0080664 R 25 0 0.994858611825 -0.640946874416 +input2.bam FBtr0080664 R 26 0 0.994858611825 -0.619158312113
--- a/test-data/input1_min20_max30_size.tab Sun Mar 31 20:58:21 2019 -0400 +++ b/test-data/input1_min20_max30_size.tab Wed Apr 10 06:38:33 2019 -0400 @@ -1,265 +1,265 @@ -Dataset Chromosome Polarity Size Counts -input1.bam FBtr0070001 F 20 4 -input1.bam FBtr0070001 F 21 4 -input1.bam FBtr0070001 F 22 29 -input1.bam FBtr0070001 F 23 15 -input1.bam FBtr0070001 F 24 1 -input1.bam FBtr0070001 R 20 0 -input1.bam FBtr0070001 R 21 0 -input1.bam FBtr0070001 R 22 0 -input1.bam FBtr0070001 R 23 0 -input1.bam FBtr0070001 R 24 0 -input1.bam FBtr0070533 F 20 2 -input1.bam FBtr0070533 F 21 2 -input1.bam FBtr0070533 F 22 4 -input1.bam FBtr0070533 F 23 2 -input1.bam FBtr0070533 F 24 0 -input1.bam FBtr0070533 F 25 1 -input1.bam FBtr0070533 R 20 0 -input1.bam FBtr0070533 R 21 0 -input1.bam FBtr0070533 R 22 0 -input1.bam FBtr0070533 R 23 0 -input1.bam FBtr0070533 R 24 0 -input1.bam FBtr0070533 R 25 0 -input1.bam FBtr0070603 F 20 6 -input1.bam FBtr0070603 F 21 3 -input1.bam FBtr0070603 F 22 3 -input1.bam FBtr0070603 F 23 10 -input1.bam FBtr0070603 F 24 2 -input1.bam FBtr0070603 F 25 5 -input1.bam FBtr0070603 F 26 5 -input1.bam FBtr0070603 F 27 3 -input1.bam FBtr0070603 R 20 0 -input1.bam FBtr0070603 R 21 0 -input1.bam FBtr0070603 R 22 0 -input1.bam FBtr0070603 R 23 0 -input1.bam FBtr0070603 R 24 0 -input1.bam FBtr0070603 R 25 0 -input1.bam FBtr0070603 R 26 0 -input1.bam FBtr0070603 R 27 0 -input1.bam FBtr0070604 F 21 1 -input1.bam FBtr0070604 F 22 23 -input1.bam FBtr0070604 F 23 10 -input1.bam FBtr0070604 R 21 0 -input1.bam FBtr0070604 R 22 0 -input1.bam FBtr0070604 R 23 0 -input1.bam FBtr0070911 F 21 1 -input1.bam FBtr0070911 R 21 0 -input1.bam FBtr0078490 F 23 1 -input1.bam FBtr0078490 R 23 0 -input1.bam FBtr0078580 F 20 9 -input1.bam FBtr0078580 F 21 5 -input1.bam FBtr0078580 F 22 13 -input1.bam FBtr0078580 F 23 5 -input1.bam FBtr0078580 F 24 180 -input1.bam FBtr0078580 F 25 212 -input1.bam FBtr0078580 F 26 1 -input1.bam FBtr0078580 F 27 2 -input1.bam FBtr0078580 F 28 17 -input1.bam 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FBtr0080664 R 24 0 1.0 2.52990576277 +input1.bam FBtr0080664 R 25 0 1.0 0.149494431436 +input1.bam FBtr0080664 R 26 0 1.0 -0.471482437606 +input1.bam FBtr0080664 R 27 0 1.0 -0.885467016968 +input1.bam FBtr0080664 R 28 0 1.0 -0.678474727287
--- a/test-data/size.tab Sun Mar 31 20:58:21 2019 -0400 +++ b/test-data/size.tab Wed Apr 10 06:38:33 2019 -0400 @@ -1,1045 +1,1045 @@ -Dataset Chromosome Polarity Size Counts -input1.bam FBtr0070001 F 16 2 -input1.bam FBtr0070001 F 17 1 -input1.bam FBtr0070001 F 18 0 -input1.bam FBtr0070001 F 19 1 -input1.bam FBtr0070001 F 20 4 -input1.bam FBtr0070001 F 21 4 -input1.bam FBtr0070001 F 22 29 -input1.bam FBtr0070001 F 23 15 -input1.bam FBtr0070001 F 24 1 -input1.bam FBtr0070001 R 16 0 -input1.bam FBtr0070001 R 17 0 -input1.bam FBtr0070001 R 18 0 -input1.bam FBtr0070001 R 19 0 -input1.bam FBtr0070001 R 20 0 -input1.bam FBtr0070001 R 21 0 -input1.bam FBtr0070001 R 22 0 -input1.bam FBtr0070001 R 23 0 -input1.bam FBtr0070001 R 24 0 -input1.bam FBtr0070533 F 15 2 -input1.bam FBtr0070533 F 16 1 -input1.bam FBtr0070533 F 17 1 -input1.bam FBtr0070533 F 18 6 -input1.bam FBtr0070533 F 19 3 -input1.bam FBtr0070533 F 20 2 -input1.bam FBtr0070533 F 21 2 -input1.bam FBtr0070533 F 22 4 -input1.bam FBtr0070533 F 23 2 -input1.bam FBtr0070533 F 24 0 -input1.bam FBtr0070533 F 25 1 -input1.bam FBtr0070533 R 15 0 -input1.bam FBtr0070533 R 16 0 -input1.bam FBtr0070533 R 17 0 -input1.bam FBtr0070533 R 18 0 -input1.bam FBtr0070533 R 19 0 -input1.bam FBtr0070533 R 20 0 -input1.bam FBtr0070533 R 21 0 -input1.bam FBtr0070533 R 22 0 -input1.bam FBtr0070533 R 23 0 -input1.bam FBtr0070533 R 24 0 -input1.bam FBtr0070533 R 25 0 -input1.bam FBtr0070603 F 15 9 -input1.bam FBtr0070603 F 16 6 -input1.bam FBtr0070603 F 17 10 -input1.bam FBtr0070603 F 18 7 -input1.bam FBtr0070603 F 19 1 -input1.bam FBtr0070603 F 20 6 -input1.bam FBtr0070603 F 21 3 -input1.bam FBtr0070603 F 22 3 -input1.bam FBtr0070603 F 23 10 -input1.bam FBtr0070603 F 24 2 -input1.bam FBtr0070603 F 25 5 -input1.bam FBtr0070603 F 26 5 -input1.bam FBtr0070603 F 27 3 -input1.bam FBtr0070603 R 15 0 -input1.bam FBtr0070603 R 16 0 -input1.bam FBtr0070603 R 17 0 -input1.bam FBtr0070603 R 18 0 -input1.bam FBtr0070603 R 19 0 -input1.bam 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FBtr0070911 F 21 1 -input1.bam FBtr0070911 R 15 0 -input1.bam FBtr0070911 R 16 0 -input1.bam FBtr0070911 R 17 0 -input1.bam FBtr0070911 R 18 0 -input1.bam FBtr0070911 R 19 0 -input1.bam FBtr0070911 R 20 0 -input1.bam FBtr0070911 R 21 0 -input1.bam FBtr0078490 F 15 3 -input1.bam FBtr0078490 F 16 3 -input1.bam FBtr0078490 F 17 0 -input1.bam FBtr0078490 F 18 1 -input1.bam FBtr0078490 F 19 0 -input1.bam FBtr0078490 F 20 0 -input1.bam FBtr0078490 F 21 0 -input1.bam FBtr0078490 F 22 0 -input1.bam FBtr0078490 F 23 1 -input1.bam FBtr0078490 R 15 0 -input1.bam FBtr0078490 R 16 0 -input1.bam FBtr0078490 R 17 0 -input1.bam FBtr0078490 R 18 0 -input1.bam FBtr0078490 R 19 0 -input1.bam FBtr0078490 R 20 0 -input1.bam FBtr0078490 R 21 0 -input1.bam FBtr0078490 R 22 0 -input1.bam FBtr0078490 R 23 0 -input1.bam FBtr0078580 F 15 592 -input1.bam FBtr0078580 F 16 20 -input1.bam FBtr0078580 F 17 31 -input1.bam FBtr0078580 F 18 9 -input1.bam FBtr0078580 F 19 8 -input1.bam FBtr0078580 F 20 9 -input1.bam FBtr0078580 F 21 5 -input1.bam FBtr0078580 F 22 13 -input1.bam FBtr0078580 F 23 5 -input1.bam FBtr0078580 F 24 180 -input1.bam FBtr0078580 F 25 212 -input1.bam FBtr0078580 F 26 1 -input1.bam FBtr0078580 F 27 2 -input1.bam FBtr0078580 F 28 17 -input1.bam FBtr0078580 R 15 0 -input1.bam FBtr0078580 R 16 0 -input1.bam FBtr0078580 R 17 0 -input1.bam FBtr0078580 R 18 0 -input1.bam FBtr0078580 R 19 0 -input1.bam FBtr0078580 R 20 0 -input1.bam FBtr0078580 R 21 0 -input1.bam FBtr0078580 R 22 0 -input1.bam FBtr0078580 R 23 0 -input1.bam FBtr0078580 R 24 0 -input1.bam FBtr0078580 R 25 0 -input1.bam FBtr0078580 R 26 0 -input1.bam FBtr0078580 R 27 0 -input1.bam FBtr0078580 R 28 0 -input1.bam FBtr0078790 F 15 2 -input1.bam FBtr0078790 F 16 2 -input1.bam FBtr0078790 F 17 1 -input1.bam FBtr0078790 F 18 1 -input1.bam FBtr0078790 F 19 2 -input1.bam FBtr0078790 F 20 2 -input1.bam FBtr0078790 F 21 0 -input1.bam FBtr0078790 F 22 2 -input1.bam FBtr0078790 F 23 1 -input1.bam FBtr0078790 R 15 1 -input1.bam FBtr0078790 R 16 0 -input1.bam FBtr0078790 R 17 0 -input1.bam FBtr0078790 R 18 0 -input1.bam FBtr0078790 R 19 0 -input1.bam FBtr0078790 R 20 0 -input1.bam FBtr0078790 R 21 0 -input1.bam FBtr0078790 R 22 0 -input1.bam FBtr0078790 R 23 0 -input1.bam FBtr0079064 F 15 2 -input1.bam FBtr0079064 F 16 0 -input1.bam FBtr0079064 F 17 1 -input1.bam FBtr0079064 F 18 0 -input1.bam FBtr0079064 F 19 0 -input1.bam FBtr0079064 F 20 0 -input1.bam FBtr0079064 F 21 1 -input1.bam FBtr0079064 R 15 0 -input1.bam FBtr0079064 R 16 0 -input1.bam FBtr0079064 R 17 0 -input1.bam FBtr0079064 R 18 0 -input1.bam FBtr0079064 R 19 0 -input1.bam FBtr0079064 R 20 0 -input1.bam FBtr0079064 R 21 0 -input1.bam FBtr0079090 F 15 1 -input1.bam FBtr0079090 F 16 1 -input1.bam FBtr0079090 F 17 0 -input1.bam FBtr0079090 F 18 1 -input1.bam FBtr0079090 F 19 0 -input1.bam FBtr0079090 F 20 0 -input1.bam FBtr0079090 F 21 0 -input1.bam FBtr0079090 F 22 0 -input1.bam FBtr0079090 F 23 0 -input1.bam FBtr0079090 F 24 1 -input1.bam FBtr0079090 F 25 0 -input1.bam FBtr0079090 F 26 0 -input1.bam FBtr0079090 F 27 0 -input1.bam FBtr0079090 F 28 1 -input1.bam FBtr0079090 R 15 0 -input1.bam FBtr0079090 R 16 0 -input1.bam FBtr0079090 R 17 0 -input1.bam FBtr0079090 R 18 0 -input1.bam FBtr0079090 R 19 0 -input1.bam FBtr0079090 R 20 0 -input1.bam FBtr0079090 R 21 1 -input1.bam FBtr0079090 R 22 0 -input1.bam FBtr0079090 R 23 0 -input1.bam FBtr0079090 R 24 0 -input1.bam FBtr0079090 R 25 0 -input1.bam FBtr0079090 R 26 0 -input1.bam FBtr0079090 R 27 0 -input1.bam FBtr0079090 R 28 0 -input1.bam FBtr0079338 F 15 2 -input1.bam FBtr0079338 F 16 2 -input1.bam FBtr0079338 F 17 1 -input1.bam FBtr0079338 F 18 1 -input1.bam FBtr0079338 F 19 1 -input1.bam FBtr0079338 F 20 0 -input1.bam FBtr0079338 F 21 3 -input1.bam FBtr0079338 F 22 6 -input1.bam FBtr0079338 R 15 0 -input1.bam FBtr0079338 R 16 0 -input1.bam FBtr0079338 R 17 0 -input1.bam FBtr0079338 R 18 0 -input1.bam FBtr0079338 R 19 0 -input1.bam FBtr0079338 R 20 0 -input1.bam FBtr0079338 R 21 0 -input1.bam FBtr0079338 R 22 0 -input1.bam FBtr0079528 F 15 12 -input1.bam FBtr0079528 F 16 11 -input1.bam FBtr0079528 F 17 0 -input1.bam FBtr0079528 F 18 5 -input1.bam FBtr0079528 F 19 4 -input1.bam FBtr0079528 F 20 12 -input1.bam FBtr0079528 F 21 3 -input1.bam FBtr0079528 F 22 2 -input1.bam FBtr0079528 F 23 3 -input1.bam FBtr0079528 F 24 36 -input1.bam FBtr0079528 F 25 8 -input1.bam FBtr0079528 F 26 5 -input1.bam FBtr0079528 F 27 2 -input1.bam FBtr0079528 F 28 2 -input1.bam FBtr0079528 F 29 1 -input1.bam FBtr0079528 R 15 0 -input1.bam FBtr0079528 R 16 0 -input1.bam FBtr0079528 R 17 0 -input1.bam FBtr0079528 R 18 0 -input1.bam FBtr0079528 R 19 0 -input1.bam FBtr0079528 R 20 0 -input1.bam FBtr0079528 R 21 0 -input1.bam FBtr0079528 R 22 0 -input1.bam FBtr0079528 R 23 0 -input1.bam FBtr0079528 R 24 0 -input1.bam FBtr0079528 R 25 0 -input1.bam FBtr0079528 R 26 0 -input1.bam FBtr0079528 R 27 0 -input1.bam FBtr0079528 R 28 0 -input1.bam FBtr0079528 R 29 0 -input1.bam FBtr0079596 F 15 43 -input1.bam FBtr0079596 F 16 34 -input1.bam FBtr0079596 F 17 16 -input1.bam FBtr0079596 F 18 5 -input1.bam FBtr0079596 F 19 10 -input1.bam FBtr0079596 F 20 13 -input1.bam FBtr0079596 F 21 3 -input1.bam FBtr0079596 F 22 16 -input1.bam FBtr0079596 F 23 8 -input1.bam FBtr0079596 F 24 0 -input1.bam FBtr0079596 F 25 0 -input1.bam FBtr0079596 F 26 3 -input1.bam FBtr0079596 F 27 1 -input1.bam FBtr0079596 R 15 0 -input1.bam FBtr0079596 R 16 0 -input1.bam FBtr0079596 R 17 0 -input1.bam FBtr0079596 R 18 0 -input1.bam FBtr0079596 R 19 0 -input1.bam FBtr0079596 R 20 0 -input1.bam FBtr0079596 R 21 0 -input1.bam FBtr0079596 R 22 0 -input1.bam FBtr0079596 R 23 0 -input1.bam FBtr0079596 R 24 0 -input1.bam FBtr0079596 R 25 0 -input1.bam FBtr0079596 R 26 0 -input1.bam FBtr0079596 R 27 0 -input1.bam FBtr0079677 F 18 1 -input1.bam FBtr0079677 F 19 2 -input1.bam FBtr0079677 F 20 0 -input1.bam FBtr0079677 F 21 0 -input1.bam FBtr0079677 F 22 0 -input1.bam FBtr0079677 F 23 1 -input1.bam 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FBtr0079692 F 20 1 -input1.bam FBtr0079692 F 21 0 -input1.bam FBtr0079692 F 22 0 -input1.bam FBtr0079692 F 23 1 -input1.bam FBtr0079692 R 16 0 -input1.bam FBtr0079692 R 17 0 -input1.bam FBtr0079692 R 18 0 -input1.bam FBtr0079692 R 19 0 -input1.bam FBtr0079692 R 20 0 -input1.bam FBtr0079692 R 21 0 -input1.bam FBtr0079692 R 22 0 -input1.bam FBtr0079692 R 23 0 -input1.bam FBtr0079693 F 15 3 -input1.bam FBtr0079693 F 16 0 -input1.bam FBtr0079693 F 17 1 -input1.bam FBtr0079693 F 18 0 -input1.bam FBtr0079693 F 19 0 -input1.bam FBtr0079693 F 20 0 -input1.bam FBtr0079693 F 21 0 -input1.bam FBtr0079693 F 22 0 -input1.bam FBtr0079693 F 23 1 -input1.bam FBtr0079693 F 24 1 -input1.bam FBtr0079693 R 15 0 -input1.bam FBtr0079693 R 16 0 -input1.bam FBtr0079693 R 17 0 -input1.bam FBtr0079693 R 18 0 -input1.bam FBtr0079693 R 19 0 -input1.bam FBtr0079693 R 20 0 -input1.bam FBtr0079693 R 21 0 -input1.bam FBtr0079693 R 22 0 -input1.bam FBtr0079693 R 23 0 -input1.bam FBtr0079693 R 24 0 -input1.bam 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FBtr0079693 F 19 0 1.0 -0.654653670708 +input1.bam FBtr0079693 F 20 0 1.0 -0.654653670708 +input1.bam FBtr0079693 F 21 0 1.0 -0.654653670708 +input1.bam FBtr0079693 F 22 0 1.0 -0.654653670708 +input1.bam FBtr0079693 F 23 1 1.0 0.436435780472 +input1.bam FBtr0079693 F 24 1 1.0 0.436435780472 +input1.bam FBtr0079693 R 15 0 1.0 2.61861468283 +input1.bam FBtr0079693 R 16 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 17 0 1.0 0.436435780472 +input1.bam FBtr0079693 R 18 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 19 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 20 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 21 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 22 0 1.0 -0.654653670708 +input1.bam FBtr0079693 R 23 0 1.0 0.436435780472 +input1.bam FBtr0079693 R 24 0 1.0 0.436435780472 +input1.bam FBtr0079694 F 15 2 1.0 2.12132034356 +input1.bam FBtr0079694 F 16 0 1.0 -0.989949493661 +input1.bam FBtr0079694 F 17 1 1.0 0.565685424949 +input1.bam FBtr0079694 F 18 0 1.0 -0.989949493661 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FBtr0079702 F 17 0 1.0 -1.0 +input1.bam FBtr0079702 F 18 2 1.0 1.0 +input1.bam FBtr0079702 R 15 0 1.0 1.0 +input1.bam FBtr0079702 R 16 0 1.0 -1.0 +input1.bam FBtr0079702 R 17 0 1.0 -1.0 +input1.bam FBtr0079702 R 18 0 1.0 1.0 +input1.bam FBtr0079728 F 15 4 1.0 2.56205046088 +input1.bam FBtr0079728 F 16 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 17 2 1.0 0.960768922831 +input1.bam FBtr0079728 F 18 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 19 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 20 1 1.0 0.160128153805 +input1.bam FBtr0079728 F 21 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 22 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 23 0 1.0 -0.64051261522 +input1.bam FBtr0079728 F 24 1 1.0 0.160128153805 +input1.bam FBtr0079728 R 15 0 1.0 2.56205046088 +input1.bam FBtr0079728 R 16 0 1.0 -0.64051261522 +input1.bam FBtr0079728 R 17 0 1.0 0.960768922831 +input1.bam FBtr0079728 R 18 0 1.0 -0.64051261522 +input1.bam FBtr0079728 R 19 0 1.0 -0.64051261522 +input1.bam FBtr0079728 R 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0.267261241912 +input1.bam FBtr0079752 F 18 0 1.0 -1.06904496765 +input1.bam FBtr0079752 F 19 1 1.0 0.267261241912 +input1.bam FBtr0079752 F 20 2 1.0 1.60356745147 +input1.bam FBtr0079752 F 21 0 1.0 -1.06904496765 +input1.bam FBtr0079752 F 22 0 1.0 -1.06904496765 +input1.bam FBtr0079752 F 23 0 1.0 -1.06904496765 +input1.bam FBtr0079752 F 24 1 1.0 0.267261241912 +input1.bam FBtr0079752 R 15 0 1.0 1.60356745147 +input1.bam FBtr0079752 R 16 0 1.0 0.267261241912 +input1.bam FBtr0079752 R 17 0 1.0 0.267261241912 +input1.bam FBtr0079752 R 18 0 1.0 -1.06904496765 +input1.bam FBtr0079752 R 19 0 1.0 0.267261241912 +input1.bam FBtr0079752 R 20 0 1.0 1.60356745147 +input1.bam FBtr0079752 R 21 0 1.0 -1.06904496765 +input1.bam FBtr0079752 R 22 0 1.0 -1.06904496765 +input1.bam FBtr0079752 R 23 0 1.0 -1.06904496765 +input1.bam FBtr0079752 R 24 0 1.0 0.267261241912 +input1.bam FBtr0079820 F 15 2 1.0 0.520305902373 +input1.bam FBtr0079820 F 16 1 1.0 -0.222988243874 +input1.bam FBtr0079820 F 17 0 1.0 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