diff --git a/CHANGELOG.md b/CHANGELOG.md index b7ff96cb..1e1eeb34 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +1. Fixed a bug where Gene score distribution graph did not appear correctly [#125](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/125) + ### `Dependencies` 1. Nextflow!>=23.04.0 diff --git a/bin/report_modules/parsers/genometools_gt_stat_parser.py b/bin/report_modules/parsers/genometools_gt_stat_parser.py index 13f975a5..9881f576 100644 --- a/bin/report_modules/parsers/genometools_gt_stat_parser.py +++ b/bin/report_modules/parsers/genometools_gt_stat_parser.py @@ -22,7 +22,6 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): data = {"GENOMETOOLS_GT_STAT": []} for report_path in list_of_report_files: - NUM_GROUPS = -1 ( report_table_dict, @@ -35,7 +34,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) = extract_report_data(report_path, NUM_GROUPS) gene_length_distribution_graph = "" - if gene_length_distribution != []: + if len(gene_length_distribution) > 1: gene_length_distribution_graph = create_dist_graph( gene_length_distribution, "Length", @@ -44,7 +43,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) gene_score_distribution_graph = "" - if gene_score_distribution != []: + if len(gene_score_distribution) > 1: gene_score_distribution_graph = create_dist_graph( gene_score_distribution, "Score", @@ -53,7 +52,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) exon_length_distribution_graph = "" - if exon_length_distribution != []: + if len(exon_length_distribution) > 1: exon_length_distribution_graph = create_dist_graph( exon_length_distribution, "Length", @@ -62,7 +61,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) exon_number_distribution_graph = "" - if exon_number_distribution != []: + if len(exon_number_distribution) > 1: exon_number_distribution_graph = create_dist_graph( exon_number_distribution, "Number", @@ -71,7 +70,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) intron_length_distribution_graph = "" - if intron_length_distribution != []: + if len(intron_length_distribution) > 1: intron_length_distribution_graph = create_dist_graph( intron_length_distribution, "Length", @@ -80,7 +79,7 @@ def parse_genometools_gt_stat_folder(folder_name="genometools_gt_stat"): ) cds_length_distribution_graph = "" - if cds_length_distribution != []: + if len(cds_length_distribution) > 1: cds_length_distribution_graph = create_dist_graph( cds_length_distribution, "Length", @@ -196,7 +195,6 @@ def extract_report_data(report_path, num_groups): def create_frequency_groups(data, num_groups): - if num_groups == -1: sorted_data = sorted(data, key=lambda x: x[0]) return [ @@ -282,7 +280,6 @@ def test_create_frequency_groups_repeat(): def create_dist_graph(groups_dict, x_label, title, file_name): - x_list = [i["stop"] for i in groups_dict] y_list = [i["freq"] for i in groups_dict] sum_y = float(sum(y_list)) @@ -299,41 +296,46 @@ def create_dist_graph(groups_dict, x_label, title, file_name): plt.gca().spines["top"].set_visible(False) plt.gca().spines["right"].set_visible(False) - min_x, min_y = (min(x_list), min(y_list)) - x_anno_step = int(float(max(x_list)) * 0.1) - ax.annotate( - f"(<={min_x}, {round(min_y, 2)}%)", - xy=(min_x, min_y), - xytext=(min_x + x_anno_step, min_y + 10), - arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), - ) + if len(y_list) >= 10: + max_x = max(x_list) + min_x, min_y = (min(x_list), min(y_list)) + x_anno_step = int(float(max(x_list)) * 0.1) + ax.annotate( + f"(<={min_x}, {round(min_y, 2)}%)", + xy=(min_x, min_y), + xytext=(min_x + x_anno_step, min_y + 10), + arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), + ) - near_50 = min([y for y in y_list if y >= 50.0]) - min_x, min_y = (x_list[y_list.index(near_50)], near_50) - ax.annotate( - f"(<={min_x}, {round(min_y, 2)}%)", - xy=(min_x, min_y), - xytext=(min_x + x_anno_step, min_y), - arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), - ) + near_50 = min([y for y in y_list if y >= 50.0]) + min_x, min_y = (x_list[y_list.index(near_50)], near_50) + ax.annotate( + f"(<={min_x}, {round(min_y, 2)}%)", + xy=(min_x, min_y), + xytext=(min_x + x_anno_step, min_y), + arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), + ) - near_90 = min([y for y in y_list if y >= 90.0]) - min_x, min_y = (x_list[y_list.index(near_90)], near_90) - ax.annotate( - f"(<={min_x}, {round(min_y, 2)}%)", - xy=(min_x, min_y), - xytext=(min_x + x_anno_step, min_y - 10), - arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), - ) + near_90 = min([y for y in y_list if y >= 90.0]) + min_x, min_y = (x_list[y_list.index(near_90)], near_90) + ax.annotate( + f"(<={min_x}, {round(min_y, 2)}%)", + xy=(min_x, min_y), + xytext=(min_x + x_anno_step, min_y - 10), + arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), + ) - near_3_sigma = min([y for y in y_list if y >= 99.7]) - min_x, min_y = (x_list[y_list.index(near_3_sigma)], near_3_sigma) - ax.annotate( - f"(<={min_x}, {round(min_y, 2)}%)", - xy=(min_x, min_y), - xytext=(min_x + x_anno_step, min_y - 10), - arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), - ) + near_3_sigma = min([y for y in y_list if y >= 99.7]) + min_x, min_y = (x_list[y_list.index(near_3_sigma)], near_3_sigma) + x_anno_step_updated = ( + x_anno_step if ((min_x + 2 * x_anno_step) < max_x) else (-2 * x_anno_step) + ) + ax.annotate( + f"(<={min_x}, {round(min_y, 2)}%)", + xy=(min_x, min_y), + xytext=(min_x + x_anno_step_updated, min_y - 10), + arrowprops=dict(color="red", arrowstyle="->, head_width=.15"), + ) plt.savefig(file_name, dpi=300) diff --git a/tests/tiny/assemblysheet.csv b/tests/tiny/assemblysheet.csv new file mode 100644 index 00000000..196f70e4 --- /dev/null +++ b/tests/tiny/assemblysheet.csv @@ -0,0 +1,2 @@ +tag,fasta,gff3 +sarscov2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gff3 diff --git a/tests/tiny/params.json b/tests/tiny/params.json new file mode 100644 index 00000000..58137a9b --- /dev/null +++ b/tests/tiny/params.json @@ -0,0 +1,8 @@ +{ + "config_profile_name": "Test profile", + "config_profile_description": "Tiny test dataset to check pipeline function", + "input": "tests/tiny/assemblysheet.csv", + "max_cpus": 2, + "max_memory": "6.GB", + "max_time": "6.h" +}