Mercurial > repos > artbio > small_rna_maps
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(-) [+] |
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--- 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" />
--- /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 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--- 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 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--- 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