# HG changeset patch # User artbio # Date 1542146626 18000 # Node ID 600e2498bd21726dce278dd489beb823e3c1f1eb # Parent 82fedc57602484982cbf3890bcef7c47fe4e24b3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty diff -r 82fedc576024 -r 600e2498bd21 small_rna_maps.py --- 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, 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, , + Writer of a tabular file + Dataset, Chromosome, Chrom_length, , 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, + + 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__": diff -r 82fedc576024 -r 600e2498bd21 small_rna_maps.xml --- 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 @@ - + numpy @@ -14,57 +14,61 @@ = ${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' ]]> @@ -78,13 +82,12 @@ value="0" help="default value: 0" /> - + @@ -118,6 +121,11 @@ + + + + - + @@ -151,20 +159,18 @@ - - + - @@ -173,59 +179,56 @@ - + + + - - - - + + - + - - + - - + - - + @@ -236,13 +239,12 @@ - - + @@ -253,7 +255,6 @@ - @@ -264,7 +265,7 @@ - + @@ -291,13 +292,12 @@ - - + @@ -308,14 +308,13 @@ - - + @@ -326,7 +325,6 @@ - diff -r 82fedc576024 -r 600e2498bd21 test-data/clustering.pdf Binary file test-data/clustering.pdf has changed diff -r 82fedc576024 -r 600e2498bd21 test-data/clustering.tab --- /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 +input1.bam FBtr0078790 73 73 F 0 73-73 1 0.0 +input1.bam FBtr0079064 72 2 F 2 1-3 3 0.666666666667 +input1.bam FBtr0079064 72 33 F 1 33-33 1 1.0 +input1.bam FBtr0079064 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079064 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079090 72 1 F 2 1-1 1 2.0 +input1.bam FBtr0079090 72 26 F 1 26-26 1 1.0 +input1.bam FBtr0079090 72 33 F 1 33-33 1 1.0 +input1.bam FBtr0079090 72 53 F 1 53-53 1 1.0 +input1.bam FBtr0079090 72 56 R 1 56-56 1 1.0 +input1.bam FBtr0079090 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079338 73 1 F 0 1-1 1 0.0 +input1.bam FBtr0079338 73 14 F 5 12-17 6 0.833333333333 +input1.bam FBtr0079338 73 25 F 1 25-25 1 1.0 +input1.bam FBtr0079338 73 44 F 10 42-46 5 2.0 +input1.bam FBtr0079338 73 73 F 0 73-73 1 0.0 +input1.bam FBtr0079528 71 9 F 97 1-18 18 5.38888888889 +input1.bam FBtr0079528 71 28 F 1 28-28 1 1.0 +input1.bam FBtr0079528 71 36 F 3 35-37 3 1.0 +input1.bam FBtr0079528 71 51 F 5 51-51 1 5.0 +input1.bam FBtr0079528 71 71 F 0 71-71 1 0.0 +input1.bam FBtr0079596 73 10 F 148 1-19 19 7.78947368421 +input1.bam FBtr0079596 73 53 F 4 53-54 2 2.0 +input1.bam FBtr0079596 73 73 F 0 73-73 1 0.0 +input1.bam FBtr0079677 72 3 F 2 1-5 5 0.4 +input1.bam FBtr0079677 72 52 F 2 52-53 2 1.0 +input1.bam FBtr0079677 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079690 72 1 F 1 1-1 1 1.0 +input1.bam FBtr0079690 72 24 F 2 22-27 6 0.333333333333 +input1.bam FBtr0079690 72 33 F 2 33-33 1 2.0 +input1.bam FBtr0079690 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079692 73 1 F 3 1-1 1 3.0 +input1.bam FBtr0079692 73 18 F 1 18-18 1 1.0 +input1.bam FBtr0079692 73 25 F 1 25-25 1 1.0 +input1.bam FBtr0079692 73 32 F 1 32-32 1 1.0 +input1.bam FBtr0079692 73 73 F 0 73-73 1 0.0 +input1.bam FBtr0079693 72 1 F 5 1-1 1 5.0 +input1.bam FBtr0079693 72 25 F 1 25-25 1 1.0 +input1.bam FBtr0079693 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079694 72 1 F 5 1-1 1 5.0 +input1.bam FBtr0079694 72 18 F 1 18-18 1 1.0 +input1.bam FBtr0079694 72 52 F 1 52-52 1 1.0 +input1.bam FBtr0079694 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079702 72 1 F 1 1-1 1 1.0 +input1.bam FBtr0079702 72 19 F 2 19-19 1 2.0 +input1.bam FBtr0079702 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079702 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079728 72 1 F 2 1-1 1 2.0 +input1.bam FBtr0079728 72 8 F 1 8-8 1 1.0 +input1.bam FBtr0079728 72 19 F 1 19-19 1 1.0 +input1.bam FBtr0079728 72 33 F 3 33-33 1 3.0 +input1.bam FBtr0079728 72 56 F 1 56-56 1 1.0 +input1.bam FBtr0079728 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079729 72 1 F 1 1-1 1 1.0 +input1.bam FBtr0079729 72 13 F 1 13-13 1 1.0 +input1.bam FBtr0079729 72 54 F 2 52-57 6 0.333333333333 +input1.bam FBtr0079729 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079752 72 1 F 2 1-1 1 2.0 +input1.bam FBtr0079752 72 9 F 2 7-12 6 0.333333333333 +input1.bam FBtr0079752 72 33 F 2 33-33 1 2.0 +input1.bam FBtr0079752 72 52 F 2 52-52 1 2.0 +input1.bam FBtr0079752 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0079820 74 1 F 0 1-1 1 0.0 +input1.bam FBtr0079820 74 50 F 13 45-56 12 1.08333333333 +input1.bam FBtr0079820 74 74 F 0 74-74 1 0.0 +input1.bam FBtr0080609 72 10 F 60 1-20 20 3.0 +input1.bam FBtr0080609 72 42 F 1 42-42 1 1.0 +input1.bam FBtr0080609 72 51 F 2 51-52 2 1.0 +input1.bam FBtr0080609 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0080644 72 6 F 6 1-12 12 0.5 +input1.bam FBtr0080644 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0080646 72 4 F 3 1-7 7 0.428571428571 +input1.bam FBtr0080646 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0080647 72 6 F 10 1-12 12 0.833333333333 +input1.bam FBtr0080647 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0080660 72 4 F 7 1-7 7 1.0 +input1.bam FBtr0080660 72 72 F 0 72-72 1 0.0 +input1.bam FBtr0080663 71 9 F 102 1-17 17 6.0 +input1.bam FBtr0080663 71 26 F 1 26-26 1 1.0 +input1.bam FBtr0080663 71 32 F 2 32-32 1 2.0 +input1.bam FBtr0080663 71 50 F 10 50-51 2 5.0 +input1.bam FBtr0080663 71 71 F 0 71-71 1 0.0 +input1.bam FBtr0080664 71 11 F 108 1-21 21 5.14285714286 +input1.bam FBtr0080664 71 33 F 9 28-38 11 0.818181818182 +input1.bam FBtr0080664 71 53 F 11 50-56 7 1.57142857143 +input1.bam FBtr0080664 71 71 F 0 71-71 1 0.0 diff -r 82fedc576024 -r 600e2498bd21 test-data/input1_cluster5_single_plot_coverage.pdf Binary file test-data/input1_cluster5_single_plot_coverage.pdf has changed diff -r 82fedc576024 -r 600e2498bd21 test-data/input1_coverage_cluster5.tab --- 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 @@ -Dataset Chromosome Chrom_length Coordinate Polarity Coverage -input1.bam FBtr0070001 72 1 F 1 -input1.bam FBtr0070001 72 2 F 1 -input1.bam FBtr0070001 72 3 F 1 -input1.bam FBtr0070001 72 4 F 1 -input1.bam FBtr0070001 72 5 F 1 -input1.bam FBtr0070001 72 6 F 1 -input1.bam FBtr0070001 72 7 F 7 -input1.bam FBtr0070001 72 8 F 10 -input1.bam FBtr0070001 72 9 F 10 -input1.bam FBtr0070001 72 10 F 10 -input1.bam FBtr0070001 72 11 F 12 -input1.bam FBtr0070001 72 12 F 12 -input1.bam FBtr0070001 72 13 F 12 -input1.bam FBtr0070001 72 14 F 12 -input1.bam FBtr0070001 72 15 F 12 -input1.bam FBtr0070001 72 16 F 13 -input1.bam FBtr0070001 72 17 F 14 -input1.bam FBtr0070001 72 18 F 14 -input1.bam FBtr0070001 72 19 F 14 -input1.bam FBtr0070001 72 20 F 14 -input1.bam FBtr0070001 72 21 F 14 -input1.bam FBtr0070001 72 22 F 14 -input1.bam FBtr0070001 72 23 F 13 -input1.bam FBtr0070001 72 24 F 13 -input1.bam FBtr0070001 72 25 F 13 -input1.bam FBtr0070001 72 26 F 13 -input1.bam FBtr0070001 72 27 F 14 -input1.bam FBtr0070001 72 28 F 11 -input1.bam FBtr0070001 72 29 F 8 -input1.bam FBtr0070001 72 30 F 9 -input1.bam FBtr0070001 72 31 F 18 -input1.bam FBtr0070001 72 32 F 44 -input1.bam FBtr0070001 72 33 F 44 -input1.bam FBtr0070001 72 34 F 44 -input1.bam FBtr0070001 72 35 F 43 -input1.bam FBtr0070001 72 36 F 43 -input1.bam FBtr0070001 72 37 F 43 -input1.bam FBtr0070001 72 38 F 43 -input1.bam FBtr0070001 72 39 F 43 -input1.bam FBtr0070001 72 40 F 42 -input1.bam FBtr0070001 72 41 F 42 -input1.bam FBtr0070001 72 42 F 42 -input1.bam FBtr0070001 72 43 F 42 -input1.bam FBtr0070001 72 44 F 42 -input1.bam FBtr0070001 72 45 F 42 -input1.bam FBtr0070001 72 46 F 42 -input1.bam FBtr0070001 72 47 F 42 -input1.bam FBtr0070001 72 48 F 42 -input1.bam FBtr0070001 72 49 F 42 -input1.bam FBtr0070001 72 50 F 41 -input1.bam FBtr0070001 72 51 F 40 -input1.bam FBtr0070001 72 52 F 40 -input1.bam FBtr0070001 72 53 F 39 -input1.bam FBtr0070001 72 72 F 0 -input1.bam FBtr0070533 72 1 F 1 -input1.bam FBtr0070533 72 2 F 1 -input1.bam FBtr0070533 72 3 F 1 -input1.bam FBtr0070533 72 4 F 1 -input1.bam FBtr0070533 72 5 F 1 -input1.bam FBtr0070533 72 6 F 1 -input1.bam FBtr0070533 72 7 F 1 -input1.bam FBtr0070533 72 8 F 1 -input1.bam FBtr0070533 72 9 F 1 -input1.bam FBtr0070533 72 10 F 1 -input1.bam FBtr0070533 72 11 F 1 -input1.bam FBtr0070533 72 12 F 3 -input1.bam FBtr0070533 72 13 F 3 -input1.bam FBtr0070533 72 14 F 3 -input1.bam FBtr0070533 72 15 F 4 -input1.bam FBtr0070533 72 16 F 3 -input1.bam FBtr0070533 72 17 F 3 -input1.bam FBtr0070533 72 18 F 3 -input1.bam FBtr0070533 72 19 F 8 -input1.bam FBtr0070533 72 20 F 9 -input1.bam FBtr0070533 72 21 F 10 -input1.bam 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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 diff -r 82fedc576024 -r 600e2498bd21 test-data/test/small_rna_map.bash --- 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 -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