changeset 16:600e2498bd21 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
author artbio
date Tue, 13 Nov 2018 17:03:46 -0500
parents 82fedc576024
children b28dcd4051e8
files small_rna_maps.py small_rna_maps.xml test-data/clustering.pdf test-data/clustering.tab test-data/input1_cluster5_single_plot_coverage.pdf test-data/input1_coverage_cluster5.tab test-data/test/small_rna_map.bash
diffstat 7 files changed, 241 insertions(+), 1739 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.py	Sat Oct 06 05:24:15 2018 -0400
+++ b/small_rna_maps.py	Tue Nov 13 17:03:46 2018 -0500
@@ -79,14 +79,13 @@
     def tile_map(self, map_dic, clust_distance):
         '''
         takes a map_dictionary {(chromosome,read_position,polarity):
-                                                    [read_length, ...]}
-        and retur a map_dictionary with same structure but with
-        read positions aggregated by size
+                                    [read_length, ...]}
+        and returns a map_dictionary with structure:
+        {(chromosome,read_position,polarity):
+            ([read_length, ...], [start_clust, end_clust])}
         '''
         clustered_dic = defaultdict(list)
         for chrom in self.chromosomes:
-            clustered_dic[(chrom, 1, 'F')] = []
-            clustered_dic[(chrom, self.chromosomes[chrom], 'F')] = []
             F_chrom_coord = []
             R_chrom_coord = []
             for key in map_dic:
@@ -104,19 +103,24 @@
             R_clust_values = [i for i in self.grouper(R_chrom_coord,
                                                       clust_distance)]
             R_clust_keys = [(i[-1]+i[0])/2 for i in R_clust_values]
+            # now 2 dictionnaries (F and R) with structure:
+            # {centered_coordinate: [coord1, coord2, coord3, ..]}
             F_clust_dic = dict(zip(F_clust_keys, F_clust_values))
             R_clust_dic = dict(zip(R_clust_keys, R_clust_values))
-            # {centered_coordinate: [coord1, coord2, coord3, ..]}
             for centcoor in F_clust_dic:
                 accumulator = []
                 for coor in F_clust_dic[centcoor]:
                     accumulator.extend(map_dic[(chrom, coor, 'F')])
-                clustered_dic[(chrom, centcoor, 'F')] = accumulator
+                clustered_dic[(chrom, centcoor, 'F')] = [len(accumulator), [
+                    F_clust_dic[centcoor][0],
+                    F_clust_dic[centcoor][-1]]]
             for centcoor in R_clust_dic:
                 accumulator = []
                 for coor in R_clust_dic[centcoor]:
                     accumulator.extend(map_dic[(chrom, coor, 'R')])
-                clustered_dic[(chrom, centcoor, 'R')] = accumulator
+                clustered_dic[(chrom, centcoor, 'R')] = [len(accumulator), [
+                    R_clust_dic[centcoor][0],
+                    R_clust_dic[centcoor][-1]]]
         return clustered_dic
 
     def compute_readcount(self, map_dictionary, out):
@@ -174,7 +178,7 @@
                 median_dictionary[key] = numpy.median(map_dictionary[key])
         self.write_table(median_dictionary, out)
 
-    def compute_coverage(self, map_dictionary, out, quality=10):
+    def compute_coverage(self, map_dictionary, out, quality=15):
         '''
         takes a map_dictionary as input and returns
         a coverage_dictionary {(chromosome,read_position,polarity):
@@ -218,7 +222,7 @@
 
     def write_table(self, mapdict, out):
         '''
-        Generic writer
+        Writer of a tabular file
         Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
         <some mapped value>
         out is an *open* file handler
@@ -231,8 +235,8 @@
 
     def write_size_table(self, sizedic, out):
         '''
-        Generic writer of summary values
-        Dataset, Chromosome, Chrom_length, <some category>, <some value>
+        Writer of a tabular file
+        Dataset, Chromosome, Chrom_length, <category (size)>, <some value>
         out is an *open* file handler
         '''
         for chrom in sorted(sizedic):
@@ -248,16 +252,38 @@
                     line = [str(i) for i in line]
                     out.write('\t'.join(line) + '\n')
 
+    def write_cluster_table(self, clustered_dic, out):
+        '''
+        Writer of a tabular file
+        Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
+        <some mapped value>
+        out is an *open* file handler
+        '''
+        for key in sorted(clustered_dic):
+            start = clustered_dic[key][1][0]
+            end = clustered_dic[key][1][1]
+            size = end - start + 1
+            density = float(clustered_dic[key][0]) / size
+            line = [self.sample_name, key[0], self.chromosomes[key[0]],
+                    key[1], key[2], clustered_dic[key][0],
+                    str(start) + "-" + str(end), str(size), str(density)]
+            line = [str(i) for i in line]
+            out.write('\t'.join(line) + '\n')
+
 
 def main(inputs, samples, methods, outputs, minsize, maxsize, cluster):
     for method, output in zip(methods, outputs):
-        F = open(output, 'w')
+        out = open(output, 'w')
         if method == 'Size':
             header = ["Dataset", "Chromosome", "Polarity", method, "Counts"]
+        elif cluster:
+            header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
+                      "Polarity", method, "Start-End", "Cluster Size",
+                      "density"]
         else:
             header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
                       "Polarity", method]
-        F.write('\t'.join(header) + '\n')
+        out.write('\t'.join(header) + '\n')
         for input, sample in zip(inputs, samples):
             mapobj = Map(input, sample, minsize, maxsize, cluster)
             token = {"Counts": mapobj.compute_readcount,
@@ -265,9 +291,14 @@
                      "Mean": mapobj.compute_mean,
                      "Median": mapobj.compute_median,
                      "Coverage": mapobj.compute_coverage,
-                     "Size": mapobj.compute_size}
-            token[method](mapobj.map_dict, F)
-        F.close()
+                     "Size": mapobj.compute_size,
+                     "cluster": mapobj.write_cluster_table}
+            if cluster:
+                token["cluster"](mapobj.map_dict, out)
+            else:
+                token[method](mapobj.map_dict, out)
+            #   mapobj.compute_coverage(mapobj.map_dict, out)
+        out.close()
 
 
 if __name__ == "__main__":
--- a/small_rna_maps.xml	Sat Oct 06 05:24:15 2018 -0400
+++ b/small_rna_maps.xml	Tue Nov 13 17:03:46 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.6.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.7.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -14,57 +14,61 @@
   </stdio>
   <command detect_errors="exit_code"><![CDATA[
           #for $file in $series
-              sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name';
-              samtools index '$file.inputs.name';
+              sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name' &&
+              samtools index '$file.inputs.name' &&
           #end for
           python '$__tool_directory__'/small_rna_maps.py
               --inputs
-          #for $file in $series
-              '$file.inputs.name'
-          #end for
-              --sample_names
-          #for $sample in $series
-              '$sample.inputs.name'
-          #end for
-          --minsize $minsize
-          --maxsize $maxsize
-          --cluster $cluster
-      #if str($plots_options.plots_options_selector ) == "two_plot":
-          --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
-          --outputs '$output_tab' '$extra_output_tab';
-      #elif str($plots_options.plots_options_selector ) == "global":
-          --plot_methods 'Size'
-          --outputs '$output_tab';
-      #else:
-          --plot_methods '${plots_options.first_plot}'
-          --outputs '$output_tab' ;
-      #end if
-      Rscript '$__tool_directory__'/small_rna_maps.r
-          --first_dataframe '$output_tab'
-          --extra_dataframe '$extra_output_tab'
-          --normalization
-          #set $norm = ""
-          #for $file in $series
-                 #set $norm += str($file.normalization)+' '
-          #end for
-          #set $norm = $norm[:-1]
-          '$norm'
-          #if $ylimits_cond.ylimits == "no":
-              --ymin '' --ymax ''
-          #else:
-              --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
-          #end if
-          #if str($plots_options.plots_options_selector ) == "two_plot":
-              --first_plot_method '${plots_options.first_plot}'
-              --extra_plot_method '${plots_options.extra_plot}'
-          #elif str($plots_options.plots_options_selector ) == "global":
-              --first_plot_method 'Size'
-              --extra_plot_method ''
-              --global '${plots_options.mergestrands}'
-          #else:
-              --first_plot_method '${plots_options.first_plot}'
-              --extra_plot_method ''
-          #end if
+              #for $file in $series
+                  '$file.inputs.name'
+              #end for
+                  --sample_names
+              #for $sample in $series
+                  '$sample.inputs.name'
+              #end for
+              --minsize $minsize
+              --maxsize $maxsize
+              #if str($plots_options.plots_options_selector ) == "two_plot":
+                  --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
+                  --outputs '$output_tab' '$extra_output_tab' &&
+              #elif str($plots_options.plots_options_selector ) == "global":
+                  --plot_methods 'Size'
+                  --outputs '$output_tab' &&
+              #elif str($plots_options.plots_options_selector ) == "cluster":
+                  --plot_methods 'Counts'
+                  --outputs '$output_tab'
+                  --cluster ${plots_options.cluster} &&
+              #else:
+                  --plot_methods '${plots_options.first_plot}'
+                  --outputs '$output_tab' &&
+              #end if
+
+          Rscript '$__tool_directory__'/small_rna_maps.r
+              --first_dataframe '$output_tab'
+              --extra_dataframe '$extra_output_tab'
+              --normalization
+              #set $norm = ""
+              #for $file in $series
+                     #set $norm += str($file.normalization)+' '
+              #end for
+              #set $norm = $norm[:-1]
+              '$norm'
+              #if $ylimits_cond.ylimits == "no":
+                  --ymin '' --ymax ''
+              #else:
+                  --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
+              #end if
+              #if str($plots_options.plots_options_selector ) == "two_plot":
+                  --first_plot_method '${plots_options.first_plot}'
+                  --extra_plot_method '${plots_options.extra_plot}'
+              #elif str($plots_options.plots_options_selector ) == "global":
+                  --first_plot_method 'Size'
+                  --extra_plot_method ''
+                  --global '${plots_options.mergestrands}'
+              #else:
+                  --first_plot_method '${plots_options.first_plot}'
+                  --extra_plot_method ''
+              #end if
               --output_pdf '$output_pdf'
   ]]></command>
  <inputs>
@@ -78,13 +82,12 @@
            value="0" help="default value: 0" />
     <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
            value="10000" help="default value: 10000" />
-    <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
-           value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
     <conditional name="plots_options">
         <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
             <option value="one_plot">Just one plot per chromosome</option>
             <option value="two_plot" selected="True">Two plots per chromosome</option>
             <option value="global">Global read size distributions of aligned reads</option>
+            <option value="cluster">Map read clusters</option>
         </param>
         <when value="two_plot">
             <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
@@ -118,6 +121,11 @@
                 <option value="merge">Merge forward and reverse reads</option>
             </param>
         </when>
+        <when value="cluster">
+            <param name="first_plot" type="hidden" value="Counts"/>
+            <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
+                   help="Sets the distance (in nt) below which reads are clustered to a single median position" />
+        </when>
     </conditional>
     <conditional name="ylimits_cond">
         <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
@@ -140,7 +148,7 @@
 </outputs>
 
     <tests>
-        <test>
+        <test> <!-- 1 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -151,20 +159,18 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Counts" />
             <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
             <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 2 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="ylimits" value="yes" />
             <param name="ymin" value="-5" />
             <param name="ymax" value="5" />
@@ -173,59 +179,56 @@
             <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
             <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 3 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="plots_options_selector" value="cluster" />
+            <param name="first_plot" value="Counts" />
             <param name="cluster" value="5" />
-            <param name="plots_options_selector" value="one_plot" />
-            <param name="first_plot" value="Coverage" />
-            <output file="input1_coverage_cluster5.tab" name="output_tab" />
-            <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
+            <output file="clustering.tab" name="output_tab" />
+            <output file="clustering.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 4 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
             </repeat>
             <param name="minsize" value="20" />
             <param name="maxsize" value="30" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Size" />
             <output file="input1_min20_max30_size.tab" name="output_tab" />
             <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 5 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Mean" />
             <output file="input1_mean.tab" name="output_tab" />
             <output file="input1__single_plot_mean.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 6 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Median" />
             <output file="input1_median.tab" name="output_tab" />
             <output file="input1_single_plot_median.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 7 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -236,13 +239,12 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Counts" />
             <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
             <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 8 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -253,7 +255,6 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="ylimits" value="yes" />
             <param name="ymin" value="-5" />
             <param name="ymax" value="5" />
@@ -264,7 +265,7 @@
             <output file="input1_input2_size.tab" name="extra_output_tab" />
             <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 9 -->
             <repeat name="series">
                 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -291,13 +292,12 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Coverage" />
             <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
             <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 10 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -308,14 +308,13 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="nomerge" />
             <param name="first_plot" value="Size" />
             <output file="size.tab" name="output_tab" />
             <output file="global_nomerge.pdf" name="output_pdf" />
         </test>
-        <test>
+        <test> <!-- 11 -->
             <repeat name="series">
                 <param name="inputs" value="input1.bam" ftype="bam" />
                 <param name="normalization" value="1.0" />
@@ -326,7 +325,6 @@
             </repeat>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
-            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="merge" />
             <param name="first_plot" value="Size" />
Binary file test-data/clustering.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clustering.tab	Tue Nov 13 17:03:46 2018 -0500
@@ -0,0 +1,119 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts	Start-End	Cluster Size	density
+input1.bam	FBtr0070001	72	1	F	1	1-1	1	1.0
+input1.bam	FBtr0070001	72	12	F	14	7-18	12	1.16666666667
+input1.bam	FBtr0070001	72	30	F	42	27-34	8	5.25
+input1.bam	FBtr0070001	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0070533	72	1	F	1	1-1	1	1.0
+input1.bam	FBtr0070533	72	25	F	23	12-38	27	0.851851851852
+input1.bam	FBtr0070533	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0070603	72	21	F	68	1-42	42	1.61904761905
+input1.bam	FBtr0070603	72	53	F	2	51-56	6	0.333333333333
+input1.bam	FBtr0070603	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0070604	72	1	F	1	1-1	1	1.0
+input1.bam	FBtr0070604	72	20	F	2	18-22	5	0.4
+input1.bam	FBtr0070604	72	31	F	36	30-32	3	12.0
+input1.bam	FBtr0070604	72	57	F	1	57-57	1	1.0
+input1.bam	FBtr0070604	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0070911	73	1	F	0	1-1	1	0.0
+input1.bam	FBtr0070911	73	15	F	1	15-15	1	1.0
+input1.bam	FBtr0070911	73	38	F	1	38-38	1	1.0
+input1.bam	FBtr0070911	73	73	F	0	73-73	1	0.0
+input1.bam	FBtr0078490	72	1	F	0	1-1	1	0.0
+input1.bam	FBtr0078490	72	15	F	4	13-18	6	0.666666666667
+input1.bam	FBtr0078490	72	26	F	3	25-28	4	0.75
+input1.bam	FBtr0078490	72	38	F	1	38-38	1	1.0
+input1.bam	FBtr0078490	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0078580	72	16	F	1102	1-31	31	35.5483870968
+input1.bam	FBtr0078580	72	52	F	2	52-52	1	2.0
+input1.bam	FBtr0078580	72	72	F	0	72-72	1	0.0
+input1.bam	FBtr0078790	73	1	F	1	1-1	1	1.0
+input1.bam	FBtr0078790	73	17	F	2	17-17	1	2.0
+input1.bam	FBtr0078790	73	33	F	1	33-33	1	1.0
+input1.bam	FBtr0078790	73	47	F	9	42-52	11	0.818181818182
+input1.bam	FBtr0078790	73	69	R	1	69-69	1	1.0
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Binary file test-data/input1_cluster5_single_plot_coverage.pdf has changed
--- a/test-data/input1_coverage_cluster5.tab	Sat Oct 06 05:24:15 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1603 +0,0 @@
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-input1.bam	FBtr0080644	72	7	F	4
-input1.bam	FBtr0080644	72	8	F	4
-input1.bam	FBtr0080644	72	9	F	4
-input1.bam	FBtr0080644	72	10	F	4
-input1.bam	FBtr0080644	72	11	F	4
-input1.bam	FBtr0080644	72	12	F	6
-input1.bam	FBtr0080644	72	13	F	6
-input1.bam	FBtr0080644	72	14	F	6
-input1.bam	FBtr0080644	72	15	F	6
-input1.bam	FBtr0080644	72	16	F	6
-input1.bam	FBtr0080644	72	17	F	6
-input1.bam	FBtr0080644	72	18	F	6
-input1.bam	FBtr0080644	72	19	F	6
-input1.bam	FBtr0080644	72	20	F	6
-input1.bam	FBtr0080644	72	21	F	5
-input1.bam	FBtr0080644	72	22	F	5
-input1.bam	FBtr0080644	72	23	F	4
-input1.bam	FBtr0080644	72	24	F	4
-input1.bam	FBtr0080644	72	25	F	4
-input1.bam	FBtr0080644	72	26	F	4
-input1.bam	FBtr0080644	72	27	F	4
-input1.bam	FBtr0080644	72	72	F	0
-input1.bam	FBtr0080646	72	1	F	1
-input1.bam	FBtr0080646	72	2	F	1
-input1.bam	FBtr0080646	72	3	F	1
-input1.bam	FBtr0080646	72	4	F	1
-input1.bam	FBtr0080646	72	5	F	1
-input1.bam	FBtr0080646	72	6	F	2
-input1.bam	FBtr0080646	72	7	F	3
-input1.bam	FBtr0080646	72	8	F	3
-input1.bam	FBtr0080646	72	9	F	3
-input1.bam	FBtr0080646	72	10	F	3
-input1.bam	FBtr0080646	72	11	F	3
-input1.bam	FBtr0080646	72	12	F	3
-input1.bam	FBtr0080646	72	13	F	3
-input1.bam	FBtr0080646	72	14	F	3
-input1.bam	FBtr0080646	72	15	F	3
-input1.bam	FBtr0080646	72	16	F	3
-input1.bam	FBtr0080646	72	17	F	2
-input1.bam	FBtr0080646	72	18	F	2
-input1.bam	FBtr0080646	72	19	F	2
-input1.bam	FBtr0080646	72	20	F	2
-input1.bam	FBtr0080646	72	21	F	2
-input1.bam	FBtr0080646	72	22	F	2
-input1.bam	FBtr0080646	72	23	F	2
-input1.bam	FBtr0080646	72	24	F	2
-input1.bam	FBtr0080646	72	25	F	2
-input1.bam	FBtr0080646	72	26	F	2
-input1.bam	FBtr0080646	72	27	F	2
-input1.bam	FBtr0080646	72	72	F	0
-input1.bam	FBtr0080647	72	1	F	3
-input1.bam	FBtr0080647	72	2	F	3
-input1.bam	FBtr0080647	72	3	F	4
-input1.bam	FBtr0080647	72	4	F	4
-input1.bam	FBtr0080647	72	5	F	4
-input1.bam	FBtr0080647	72	6	F	6
-input1.bam	FBtr0080647	72	7	F	6
-input1.bam	FBtr0080647	72	8	F	7
-input1.bam	FBtr0080647	72	9	F	7
-input1.bam	FBtr0080647	72	10	F	7
-input1.bam	FBtr0080647	72	11	F	9
-input1.bam	FBtr0080647	72	12	F	10
-input1.bam	FBtr0080647	72	13	F	10
-input1.bam	FBtr0080647	72	14	F	10
-input1.bam	FBtr0080647	72	15	F	10
-input1.bam	FBtr0080647	72	16	F	9
-input1.bam	FBtr0080647	72	17	F	8
-input1.bam	FBtr0080647	72	18	F	8
-input1.bam	FBtr0080647	72	19	F	6
-input1.bam	FBtr0080647	72	20	F	6
-input1.bam	FBtr0080647	72	21	F	6
-input1.bam	FBtr0080647	72	22	F	5
-input1.bam	FBtr0080647	72	23	F	5
-input1.bam	FBtr0080647	72	24	F	5
-input1.bam	FBtr0080647	72	25	F	5
-input1.bam	FBtr0080647	72	26	F	5
-input1.bam	FBtr0080647	72	27	F	5
-input1.bam	FBtr0080647	72	72	F	0
-input1.bam	FBtr0080660	72	1	F	0
-input1.bam	FBtr0080660	72	4	F	4
-input1.bam	FBtr0080660	72	5	F	4
-input1.bam	FBtr0080660	72	6	F	4
-input1.bam	FBtr0080660	72	7	F	7
-input1.bam	FBtr0080660	72	8	F	7
-input1.bam	FBtr0080660	72	9	F	7
-input1.bam	FBtr0080660	72	10	F	7
-input1.bam	FBtr0080660	72	11	F	7
-input1.bam	FBtr0080660	72	12	F	7
-input1.bam	FBtr0080660	72	13	F	7
-input1.bam	FBtr0080660	72	14	F	7
-input1.bam	FBtr0080660	72	15	F	7
-input1.bam	FBtr0080660	72	16	F	7
-input1.bam	FBtr0080660	72	17	F	7
-input1.bam	FBtr0080660	72	18	F	7
-input1.bam	FBtr0080660	72	19	F	7
-input1.bam	FBtr0080660	72	20	F	7
-input1.bam	FBtr0080660	72	21	F	7
-input1.bam	FBtr0080660	72	22	F	7
-input1.bam	FBtr0080660	72	23	F	6
-input1.bam	FBtr0080660	72	24	F	6
-input1.bam	FBtr0080660	72	25	F	6
-input1.bam	FBtr0080660	72	26	F	6
-input1.bam	FBtr0080660	72	27	F	6
-input1.bam	FBtr0080660	72	72	F	0
-input1.bam	FBtr0080663	71	1	F	22
-input1.bam	FBtr0080663	71	2	F	22
-input1.bam	FBtr0080663	71	3	F	78
-input1.bam	FBtr0080663	71	4	F	82
-input1.bam	FBtr0080663	71	5	F	82
-input1.bam	FBtr0080663	71	6	F	82
-input1.bam	FBtr0080663	71	7	F	83
-input1.bam	FBtr0080663	71	8	F	87
-input1.bam	FBtr0080663	71	9	F	87
-input1.bam	FBtr0080663	71	10	F	87
-input1.bam	FBtr0080663	71	11	F	87
-input1.bam	FBtr0080663	71	12	F	89
-input1.bam	FBtr0080663	71	13	F	89
-input1.bam	FBtr0080663	71	14	F	91
-input1.bam	FBtr0080663	71	15	F	92
-input1.bam	FBtr0080663	71	16	F	93
-input1.bam	FBtr0080663	71	17	F	89
-input1.bam	FBtr0080663	71	18	F	86
-input1.bam	FBtr0080663	71	19	F	86
-input1.bam	FBtr0080663	71	20	F	86
-input1.bam	FBtr0080663	71	21	F	86
-input1.bam	FBtr0080663	71	22	F	86
-input1.bam	FBtr0080663	71	23	F	78
-input1.bam	FBtr0080663	71	24	F	77
-input1.bam	FBtr0080663	71	25	F	77
-input1.bam	FBtr0080663	71	26	F	70
-input1.bam	FBtr0080663	71	27	F	34
-input1.bam	FBtr0080663	71	28	F	21
-input1.bam	FBtr0080663	71	29	F	14
-input1.bam	FBtr0080663	71	30	F	14
-input1.bam	FBtr0080663	71	31	F	13
-input1.bam	FBtr0080663	71	32	F	7
-input1.bam	FBtr0080663	71	33	F	4
-input1.bam	FBtr0080663	71	34	F	4
-input1.bam	FBtr0080663	71	35	F	3
-input1.bam	FBtr0080663	71	36	F	3
-input1.bam	FBtr0080663	71	37	F	3
-input1.bam	FBtr0080663	71	38	F	3
-input1.bam	FBtr0080663	71	39	F	3
-input1.bam	FBtr0080663	71	40	F	3
-input1.bam	FBtr0080663	71	41	F	3
-input1.bam	FBtr0080663	71	42	F	3
-input1.bam	FBtr0080663	71	43	F	3
-input1.bam	FBtr0080663	71	44	F	2
-input1.bam	FBtr0080663	71	45	F	2
-input1.bam	FBtr0080663	71	46	F	2
-input1.bam	FBtr0080663	71	47	F	1
-input1.bam	FBtr0080663	71	50	F	1
-input1.bam	FBtr0080663	71	51	F	10
-input1.bam	FBtr0080663	71	52	F	10
-input1.bam	FBtr0080663	71	53	F	10
-input1.bam	FBtr0080663	71	54	F	10
-input1.bam	FBtr0080663	71	55	F	10
-input1.bam	FBtr0080663	71	56	F	10
-input1.bam	FBtr0080663	71	57	F	10
-input1.bam	FBtr0080663	71	58	F	10
-input1.bam	FBtr0080663	71	59	F	10
-input1.bam	FBtr0080663	71	60	F	10
-input1.bam	FBtr0080663	71	61	F	10
-input1.bam	FBtr0080663	71	62	F	10
-input1.bam	FBtr0080663	71	63	F	10
-input1.bam	FBtr0080663	71	64	F	10
-input1.bam	FBtr0080663	71	65	F	10
-input1.bam	FBtr0080663	71	66	F	2
-input1.bam	FBtr0080663	71	67	F	1
-input1.bam	FBtr0080663	71	68	F	1
-input1.bam	FBtr0080663	71	69	F	1
-input1.bam	FBtr0080663	71	70	F	1
-input1.bam	FBtr0080663	71	71	F	0
-input1.bam	FBtr0080664	71	1	F	16
-input1.bam	FBtr0080664	71	2	F	16
-input1.bam	FBtr0080664	71	3	F	72
-input1.bam	FBtr0080664	71	4	F	76
-input1.bam	FBtr0080664	71	5	F	76
-input1.bam	FBtr0080664	71	6	F	77
-input1.bam	FBtr0080664	71	7	F	78
-input1.bam	FBtr0080664	71	8	F	82
-input1.bam	FBtr0080664	71	9	F	83
-input1.bam	FBtr0080664	71	10	F	83
-input1.bam	FBtr0080664	71	11	F	86
-input1.bam	FBtr0080664	71	12	F	89
-input1.bam	FBtr0080664	71	13	F	91
-input1.bam	FBtr0080664	71	14	F	94
-input1.bam	FBtr0080664	71	15	F	94
-input1.bam	FBtr0080664	71	16	F	95
-input1.bam	FBtr0080664	71	17	F	100
-input1.bam	FBtr0080664	71	18	F	98
-input1.bam	FBtr0080664	71	19	F	97
-input1.bam	FBtr0080664	71	20	F	97
-input1.bam	FBtr0080664	71	21	F	97
-input1.bam	FBtr0080664	71	22	F	97
-input1.bam	FBtr0080664	71	23	F	93
-input1.bam	FBtr0080664	71	24	F	88
-input1.bam	FBtr0080664	71	25	F	88
-input1.bam	FBtr0080664	71	26	F	82
-input1.bam	FBtr0080664	71	27	F	47
-input1.bam	FBtr0080664	71	28	F	33
-input1.bam	FBtr0080664	71	29	F	23
-input1.bam	FBtr0080664	71	30	F	23
-input1.bam	FBtr0080664	71	31	F	20
-input1.bam	FBtr0080664	71	32	F	13
-input1.bam	FBtr0080664	71	33	F	6
-input1.bam	FBtr0080664	71	34	F	7
-input1.bam	FBtr0080664	71	35	F	8
-input1.bam	FBtr0080664	71	36	F	7
-input1.bam	FBtr0080664	71	37	F	8
-input1.bam	FBtr0080664	71	38	F	9
-input1.bam	FBtr0080664	71	39	F	9
-input1.bam	FBtr0080664	71	40	F	9
-input1.bam	FBtr0080664	71	41	F	9
-input1.bam	FBtr0080664	71	42	F	9
-input1.bam	FBtr0080664	71	43	F	9
-input1.bam	FBtr0080664	71	44	F	7
-input1.bam	FBtr0080664	71	45	F	7
-input1.bam	FBtr0080664	71	46	F	7
-input1.bam	FBtr0080664	71	47	F	6
-input1.bam	FBtr0080664	71	48	F	6
-input1.bam	FBtr0080664	71	49	F	6
-input1.bam	FBtr0080664	71	50	F	6
-input1.bam	FBtr0080664	71	51	F	13
-input1.bam	FBtr0080664	71	52	F	14
-input1.bam	FBtr0080664	71	53	F	12
-input1.bam	FBtr0080664	71	54	F	12
-input1.bam	FBtr0080664	71	55	F	11
-input1.bam	FBtr0080664	71	56	F	12
-input1.bam	FBtr0080664	71	57	F	11
-input1.bam	FBtr0080664	71	58	F	11
-input1.bam	FBtr0080664	71	59	F	11
-input1.bam	FBtr0080664	71	60	F	11
-input1.bam	FBtr0080664	71	61	F	11
-input1.bam	FBtr0080664	71	62	F	11
-input1.bam	FBtr0080664	71	63	F	11
-input1.bam	FBtr0080664	71	64	F	11
-input1.bam	FBtr0080664	71	65	F	11
-input1.bam	FBtr0080664	71	66	F	2
-input1.bam	FBtr0080664	71	67	F	1
-input1.bam	FBtr0080664	71	68	F	1
-input1.bam	FBtr0080664	71	69	F	1
-input1.bam	FBtr0080664	71	70	F	1
-input1.bam	FBtr0080664	71	71	F	1
--- a/test-data/test/small_rna_map.bash	Sat Oct 06 05:24:15 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-#! /bin/bash
-# Execution command : bash small_rna_map.bash <sam file>
-samtools view -h -o input.sam ../test-data/input.bam
-samfile="input.sam"
-cut -f2,3,4,5,6 ../test-data/output.tab > test-data.dat
-grep -e "^@SQ" $samfile > header.tab
-cat $samfile | perl -ne 'print unless /^@/ or ( (split /\t/)[1] != 0 and (split /\t/)[1] != 16 )' > output1.tab
-
-cat << EOF > pyscript.py
-lendic = {}
-for line in open("header.tab"):
-  fields = line[:-1].split()
-  lendic[fields[1][3:]] = fields[2][3:]
-readdic = {}
-for line in (open("output1.tab")):
-  fields = line[:-1].split()
-  key = "-".join([fields[2],fields[3],"F" if fields[1]=="0" else "R"])
-  try:
-    readdic[key] += 1
-  except KeyError:
-    readdic[key] = 1
-Out = open("output.tab", "w")
-Out.write("Chromosome\tChrom_length\tCoordinate\tNbr_reads\tPolarity\n")
-for key in sorted(readdic):
-  fields = key.split("-")
-  Chromosome, Coordinate, Polarity = fields[0], fields[1], fields[2]
-  Chrom_length = lendic[Chromosome]
-  Nbr_reads = str(readdic[key])
-  Out.write("\t".join([Chromosome, Chrom_length, Coordinate, Nbr_reads, Polarity]) )
-  Out.write("\n")
-Out.close
-EOF
-
-python ./pyscript.py
-rm output1.tab header.tab pyscript.py
-sort -k 1,1 -k 3,3n -k 5,5  output.tab -o output.tab
-if ! diff -q output.tab test-data.dat &>/dev/null; then
-  >&2 echo "different"
-else
-  >&2 echo "Test passed"
-fi
-
-rm output.tab input.sam test-data.dat