Mercurial > repos > artbio > small_rna_maps

changeset 9:3ea75c573429 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
author artbio
date Tue, 07 Nov 2017 12:31:28 -0500
parents 1827b74f872b
children c3fb2a864526
files small_rna_maps.py small_rna_maps.xml test-data/count_cluster_5.pdf test-data/count_cluster_5.tab
diffstat 4 files changed, 361 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.py	Mon Oct 23 08:29:39 2017 -0400
+++ b/small_rna_maps.py	Tue Nov 07 12:31:28 2017 -0500
@@ -14,6 +14,8 @@
                             default=0, help='minimal size of reads')
     the_parser.add_argument('--maxsize', dest='maxsize', type=int,
                             default=10000, help='maximal size of reads')
+    the_parser.add_argument('--cluster', dest='cluster', type=int,
+                            default=0, help='clustering distance')
     the_parser.add_argument('--sample_names', dest='sample_names',
                             required=True, nargs='+',
                             help='list of sample names')
@@ -28,15 +30,18 @@
 
 class Map:
 
-    def __init__(self, bam_file, sample, minsize, maxsize):
+    def __init__(self, bam_file, sample, minsize, maxsize, cluster):
         self.sample_name = sample
         self.minsize = minsize
         self.maxsize = maxsize
+        self.cluster = cluster
         self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
         self.chromosomes = dict(zip(self.bam_object.references,
                                 self.bam_object.lengths))
         self.map_dict = self.create_map(self.bam_object, self.minsize,
                                         self.maxsize)
+        if self.cluster:
+            self.map_dict = self.tile_map(self.map_dict, self.cluster)
 
     def create_map(self, bam_object, minsize, maxsize):
         '''
@@ -44,11 +49,10 @@
                                                     [read_length, ...]}
         '''
         map_dictionary = defaultdict(list)
-        # get empty value for start and end of each chromosome
         for chrom in self.chromosomes:
+            # get empty value for start and end of each chromosome
             map_dictionary[(chrom, 1, 'F')] = []
             map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
-        for chrom in self.chromosomes:
             for read in bam_object.fetch(chrom):
                 if (read.query_alignment_length >= minsize and
                         read.query_alignment_length <= maxsize):
@@ -61,6 +65,62 @@
                                         read.query_alignment_length)
         return map_dictionary
 
+    def grouper(self, iterable, clust_distance):
+        prev = None
+        group = []
+        for item in iterable:
+            if not prev or item - prev <= clust_distance:
+                group.append(item)
+            else:
+                yield group
+                group = [item]
+            prev = item
+        if group:
+            yield group
+
+    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
+        '''
+        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:
+                if key[0] == chrom and key[2] == 'F':
+                    F_chrom_coord.append(key[1])
+                elif key[0] == chrom and key[2] == 'R':
+                    R_chrom_coord.append(key[1])
+            F_chrom_coord = list(set(F_chrom_coord))
+            R_chrom_coord = list(set(R_chrom_coord))
+            F_chrom_coord.sort()
+            R_chrom_coord.sort()
+            F_clust_values = [i for i in self.grouper(F_chrom_coord,
+                                                      clust_distance)]
+            F_clust_keys = [(i[-1]+i[0])/2 for i in F_clust_values]
+            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]
+            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
+            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
+        return clustered_dic
+
     def compute_readcount(self, map_dictionary, out):
         '''
         takes a map_dictionary as input and writes
@@ -191,7 +251,7 @@
                     out.write('\t'.join(line) + '\n')
 
 
-def main(inputs, samples, methods, outputs, minsize, maxsize):
+def main(inputs, samples, methods, outputs, minsize, maxsize, cluster):
     for method, output in zip(methods, outputs):
         F = open(output, 'w')
         if method == 'Size':
@@ -201,7 +261,7 @@
                       "Polarity", method]
         F.write('\t'.join(header) + '\n')
         for input, sample in zip(inputs, samples):
-            mapobj = Map(input, sample, minsize, maxsize)
+            mapobj = Map(input, sample, minsize, maxsize, cluster)
             token = {"Counts": mapobj.compute_readcount,
                      "Max": mapobj.compute_max,
                      "Mean": mapobj.compute_mean,
@@ -219,4 +279,4 @@
         args.sample_names = [name + '_' + str(i) for
                              i, name in enumerate(args.sample_names)]
     main(args.inputs, args.sample_names, args.plot_methods, args.outputs,
-         args.minsize, args.maxsize)
+         args.minsize, args.maxsize, args.cluster)
--- a/small_rna_maps.xml	Mon Oct 23 08:29:39 2017 -0400
+++ b/small_rna_maps.xml	Tue Nov 07 12:31:28 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.3.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.4.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -27,6 +27,7 @@
       #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' &&
@@ -62,6 +63,8 @@
            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>
@@ -115,7 +118,19 @@
         <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
+            <param name="cluster" value="5" />
             <param name="maxsize" value="10000" />
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="normalization" value="1 1" />
+            <param name="first_plot" value="Counts" />
+            <output file="count_cluster_5.tab" name="output_tab" />
+            <output file="count_cluster_5.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
+            <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" />
@@ -127,6 +142,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <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" />
@@ -138,6 +154,7 @@
             <param name="inputs" value="input1.bam" ftype="bam"/>
             <param name="minsize" value="20" />
             <param name="maxsize" value="30" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="merge" />
             <param name="first_plot" value="Size" />
@@ -149,6 +166,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
@@ -161,6 +179,7 @@
             <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
             <param name="minsize" value="20" />
             <param name="maxsize" value="30" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
@@ -173,6 +192,7 @@
             <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
@@ -185,6 +205,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Median" />
@@ -197,6 +218,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Coverage" />
@@ -209,6 +231,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Size" />
@@ -221,6 +244,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Size" />
             <param name="extra_plot" value="Counts" />
@@ -233,6 +257,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
             <param name="maxsize" value="10000" />
+            <param name="cluster" value="0" />
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Size" />
             <param name="extra_plot" value="Counts" />
@@ -244,6 +269,7 @@
         <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="minsize" value="0" />
+            <param name="cluster" value="0" />
             <param name="maxsize" value="10000" />
             <param name="plots_options_selector" value="one_plot" />
             <param name="normalization" value="1 1" />
@@ -255,6 +281,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <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="Size" />
             <param name="normalization" value="1 1" />
@@ -265,6 +292,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <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" />
             <param name="normalization" value="1 1" />
@@ -275,6 +303,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <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" />
             <param name="normalization" value="1 0.2" />
Binary file test-data/count_cluster_5.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count_cluster_5.tab	Tue Nov 07 12:31:28 2017 -0500
@@ -0,0 +1,265 @@
+Dataset	Chromosome	Chrom_length	Coordinate	Polarity	Counts
+input2.bam	FBtr0070001	72	1	F	1
+input2.bam	FBtr0070001	72	15	F	4
+input2.bam	FBtr0070001	72	30	F	4
+input2.bam	FBtr0070001	72	55	F	15
+input2.bam	FBtr0070001	72	72	F	0
+input2.bam	FBtr0070533	72	1	F	0
+input2.bam	FBtr0070533	72	21	F	44
+input2.bam	FBtr0070533	72	39	F	1
+input2.bam	FBtr0070533	72	72	F	0
+input2.bam	FBtr0070603	72	1	F	0
+input2.bam	FBtr0070603	72	26	F	57
+input2.bam	FBtr0070603	72	52	F	4
+input2.bam	FBtr0070603	72	72	F	0
+input2.bam	FBtr0070604	72	1	F	0
+input2.bam	FBtr0070604	72	2	F	1
+input2.bam	FBtr0070604	72	31	F	6
+input2.bam	FBtr0070604	72	40	F	1
+input2.bam	FBtr0070604	72	55	F	47
+input2.bam	FBtr0070604	72	72	F	0
+input2.bam	FBtr0070911	73	1	F	0
+input2.bam	FBtr0070911	73	11	F	1
+input2.bam	FBtr0070911	73	32	F	1
+input2.bam	FBtr0070911	73	48	F	1
+input2.bam	FBtr0070911	73	73	F	0
+input2.bam	FBtr0078490	72	1	F	3
+input2.bam	FBtr0078490	72	13	F	6
+input2.bam	FBtr0078490	72	20	F	1
+input2.bam	FBtr0078490	72	30	F	1
+input2.bam	FBtr0078490	72	39	F	3
+input2.bam	FBtr0078490	72	72	F	0
+input2.bam	FBtr0078580	72	1	F	146
+input2.bam	FBtr0078580	72	21	F	215
+input2.bam	FBtr0078580	72	41	F	6
+input2.bam	FBtr0078580	72	52	F	3
+input2.bam	FBtr0078580	72	72	F	0
+input2.bam	FBtr0078790	73	1	F	0
+input2.bam	FBtr0078790	73	17	F	1
+input2.bam	FBtr0078790	73	47	F	9
+input2.bam	FBtr0078790	73	73	F	0
+input2.bam	FBtr0079064	72	1	F	3
+input2.bam	FBtr0079064	72	52	F	2
+input2.bam	FBtr0079064	72	72	F	0
+input2.bam	FBtr0079090	72	1	F	1
+input2.bam	FBtr0079090	72	18	F	2
+input2.bam	FBtr0079090	72	34	F	2
+input2.bam	FBtr0079090	72	52	F	2
+input2.bam	FBtr0079090	72	72	F	0
+input2.bam	FBtr0079338	73	1	F	0
+input2.bam	FBtr0079338	73	15	F	19
+input2.bam	FBtr0079338	73	40	F	4
+input2.bam	FBtr0079338	73	73	F	0
+input2.bam	FBtr0079528	71	1	F	0
+input2.bam	FBtr0079528	71	2	F	3
+input2.bam	FBtr0079528	71	16	F	114
+input2.bam	FBtr0079528	71	43	F	248
+input2.bam	FBtr0079528	71	71	F	0
+input2.bam	FBtr0079596	73	1	F	0
+input2.bam	FBtr0079596	73	11	F	311
+input2.bam	FBtr0079596	73	42	F	1
+input2.bam	FBtr0079596	73	53	F	3
+input2.bam	FBtr0079596	73	59	R	1
+input2.bam	FBtr0079596	73	73	F	0
+input2.bam	FBtr0079677	72	1	F	2
+input2.bam	FBtr0079677	72	15	F	1
+input2.bam	FBtr0079677	72	24	F	1
+input2.bam	FBtr0079677	72	43	F	1
+input2.bam	FBtr0079677	72	53	F	2
+input2.bam	FBtr0079677	72	72	F	0
+input2.bam	FBtr0079690	72	1	F	1
+input2.bam	FBtr0079690	72	18	F	4
+input2.bam	FBtr0079690	72	72	F	0
+input2.bam	FBtr0079692	73	1	F	0
+input2.bam	FBtr0079692	73	8	F	4
+input2.bam	FBtr0079692	73	73	F	0
+input2.bam	FBtr0079693	72	1	F	3
+input2.bam	FBtr0079693	72	18	F	3
+input2.bam	FBtr0079693	72	45	F	1
+input2.bam	FBtr0079693	72	53	F	2
+input2.bam	FBtr0079693	72	72	F	0
+input2.bam	FBtr0079694	72	1	F	2
+input2.bam	FBtr0079694	72	17	F	3
+input2.bam	FBtr0079694	72	52	F	1
+input2.bam	FBtr0079694	72	72	F	0
+input2.bam	FBtr0079702	72	1	F	2
+input2.bam	FBtr0079702	72	52	F	2
+input2.bam	FBtr0079702	72	72	F	0
+input2.bam	FBtr0079728	72	1	F	3
+input2.bam	FBtr0079728	72	20	F	1
+input2.bam	FBtr0079728	72	52	F	2
+input2.bam	FBtr0079728	72	72	F	0
+input2.bam	FBtr0079729	72	1	F	1
+input2.bam	FBtr0079729	72	19	F	1
+input2.bam	FBtr0079729	72	33	F	1
+input2.bam	FBtr0079729	72	53	F	1
+input2.bam	FBtr0079729	72	72	F	0
+input2.bam	FBtr0079752	72	1	F	0
+input2.bam	FBtr0079752	72	50	F	2
+input2.bam	FBtr0079752	72	72	F	0
+input2.bam	FBtr0079820	74	1	F	0
+input2.bam	FBtr0079820	74	39	F	1
+input2.bam	FBtr0079820	74	56	F	108
+input2.bam	FBtr0079820	74	74	F	0
+input2.bam	FBtr0080609	72	1	F	0
+input2.bam	FBtr0080609	72	21	F	4
+input2.bam	FBtr0080609	72	33	F	1
+input2.bam	FBtr0080609	72	39	F	1
+input2.bam	FBtr0080609	72	52	F	2
+input2.bam	FBtr0080609	72	72	F	0
+input2.bam	FBtr0080644	72	1	F	0
+input2.bam	FBtr0080644	72	57	F	8
+input2.bam	FBtr0080644	72	72	F	0
+input2.bam	FBtr0080646	72	1	F	0
+input2.bam	FBtr0080646	72	51	F	1
+input2.bam	FBtr0080646	72	57	F	11
+input2.bam	FBtr0080646	72	72	F	0
+input2.bam	FBtr0080647	72	1	F	1
+input2.bam	FBtr0080647	72	57	F	11
+input2.bam	FBtr0080647	72	72	F	0
+input2.bam	FBtr0080660	72	1	F	0
+input2.bam	FBtr0080660	72	58	F	11
+input2.bam	FBtr0080660	72	72	F	0
+input2.bam	FBtr0080663	71	1	F	2
+input2.bam	FBtr0080663	71	16	F	95
+input2.bam	FBtr0080663	71	31	F	1
+input2.bam	FBtr0080663	71	53	F	8
+input2.bam	FBtr0080663	71	71	F	0
+input2.bam	FBtr0080664	71	1	F	0
+input2.bam	FBtr0080664	71	2	F	3
+input2.bam	FBtr0080664	71	17	F	114
+input2.bam	FBtr0080664	71	43	F	270
+input2.bam	FBtr0080664	71	62	R	1
+input2.bam	FBtr0080664	71	71	F	0
+input2.bam	FBtr0080664	71	71	R	1
+input1.bam	FBtr0070001	72	1	F	1
+input1.bam	FBtr0070001	72	12	F	14
+input1.bam	FBtr0070001	72	30	F	42
+input1.bam	FBtr0070001	72	72	F	0
+input1.bam	FBtr0070533	72	1	F	1
+input1.bam	FBtr0070533	72	25	F	23
+input1.bam	FBtr0070533	72	72	F	0
+input1.bam	FBtr0070603	72	1	F	0
+input1.bam	FBtr0070603	72	21	F	68
+input1.bam	FBtr0070603	72	53	F	2
+input1.bam	FBtr0070603	72	72	F	0
+input1.bam	FBtr0070604	72	1	F	1
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