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regex pattern do not match

Open SolayMane opened this issue 1 year ago • 2 comments

I runt the fellowing command :

 python general_read_density_data.py TE_input/Cleaned_Fusarium_oxysporum_f.sp._albedinis_Foa_44.tsv out_TE_density/ "FOA_(.*?).h5"

I got this error :

The strings of chromosomes in your unprocessed
                hdf5 files: ['Chr_1', 'Chr_10', 'Chr_10_GeneData', 'Chr_10_TEData', 'Chr_10_overlap', 'Chr_11', 'Chr_11_GeneData', 'Chr_11_TEData', 'Chr_11_overlap', 'Chr_12', 'Chr_12_GeneData', 'Chr_12_TEData', 'Chr_12_overlap', 'Chr_13', 'Chr_13_GeneData', 'Chr_13_TEData', 'Chr_13_overlap', 'Chr_1_GeneData', 'Chr_1_TEData', 'Chr_1_overlap', 'Chr_2', 'Chr_2_GeneData', 'Chr_2_TEData', 'Chr_2_overlap', 'Chr_4', 'Chr_4_GeneData', 'Chr_4_TEData', 'Chr_4_overlap', 'Chr_5', 'Chr_5_GeneData', 'Chr_5_TEData', 'Chr_5_overlap', 'Chr_7', 'Chr_7_GeneData', 'Chr_7_TEData', 'Chr_7_overlap', 'Chr_8', 'Chr_8_GeneData', 'Chr_8_TEData', 'Chr_8_overlap', 'Chr_9', 'Chr_9_GeneData', 'Chr_9_TEData', 'Chr_9_overlap', 'Contig1', 'Contig11', 'Contig11_GeneData', 'Contig11_TEData', 'Contig11_overlap', 'Contig12', 'Contig12_GeneData', 'Contig12_TEData', 'Contig12_overlap', 'Contig15', 'Contig15_GeneData', 'Contig15_TEData', 'Contig15_overlap', 'Contig17', 'Contig17_GeneData', 'Contig17_TEData', 'Contig17_overlap', 'Contig18', 'Contig18_GeneData', 'Contig18_TEData', 'Contig18_overlap', 'Contig19', 'Contig19_GeneData', 'Contig19_TEData', 'Contig19_overlap', 'Contig1_GeneData', 'Contig1_TEData', 'Contig1_overlap', 'Contig21', 'Contig21_GeneData', 'Contig21_TEData', 'Contig21_overlap', 'Contig22', 'Contig22_GeneData', 'Contig22_TEData', 'Contig22_overlap', 'Contig23', 'Contig23_GeneData', 'Contig23_TEData', 'Contig23_overlap', 'Contig24', 'Contig24_GeneData', 'Contig24_TEData', 'Contig24_overlap', 'Contig25', 'Contig25_GeneData', 'Contig25_TEData', 'Contig25_overlap', 'Contig26', 'Contig26_GeneData', 'Contig26_TEData', 'Contig26_overlap', 'Contig29', 'Contig29_GeneData', 'Contig29_TEData', 'Contig29_overlap', 'Contig3', 'Contig31', 'Contig31_GeneData', 'Contig31_TEData', 'Contig31_overlap', 'Contig32', 'Contig32_GeneData', 'Contig32_TEData', 'Contig32_overlap', 'Contig33', 'Contig33_GeneData', 'Contig33_TEData', 'Contig33_overlap', 'Contig34', 'Contig34_GeneData', 'Contig34_TEData', 'Contig34_overlap', 'Contig36', 'Contig36_GeneData', 'Contig36_TEData', 'Contig36_overlap', 'Contig38', 'Contig38_GeneData', 'Contig38_TEData', 'Contig38_overlap', 'Contig3_GeneData', 'Contig3_TEData', 'Contig3_overlap', 'Contig4', 'Contig42', 'Contig42_GeneData', 'Contig42_TEData', 'Contig42_overlap', 'Contig46', 'Contig46_GeneData', 'Contig46_TEData', 'Contig46_overlap', 'Contig49', 'Contig49_GeneData', 'Contig49_TEData', 'Contig49_overlap', 'Contig4_GeneData', 'Contig4_TEData', 'Contig4_overlap', 'Contig50', 'Contig50_GeneData', 'Contig50_TEData', 'Contig50_overlap', 'Contig51', 'Contig51_GeneData', 'Contig51_TEData', 'Contig51_overlap', 'Contig52', 'Contig52_GeneData', 'Contig52_TEData', 'Contig52_overlap', 'Contig54', 'Contig54_GeneData', 'Contig54_TEData', 'Contig54_overlap', 'Contig56', 'Contig56_GeneData', 'Contig56_TEData', 'Contig56_overlap', 'Contig59', 'Contig59_GeneData', 'Contig59_TEData', 'Contig59_overlap', 'Contig62', 'Contig62_GeneData', 'Contig62_TEData', 'Contig62_overlap', 'Contig65', 'Contig65_GeneData', 'Contig65_TEData', 'Contig65_overlap', 'Contig67', 'Contig67_GeneData', 'Contig67_TEData', 'Contig67_overlap', 'Contig68', 'Contig68_GeneData', 'Contig68_TEData', 'Contig68_overlap', 'Contig69', 'Contig69_GeneData', 'Contig69_TEData', 'Contig69_overlap', 'Contig7', 'Contig7_GeneData', 'Contig7_TEData', 'Contig7_overlap', 'Contig8', 'Contig8_GeneData', 'Contig8_TEData', 'Contig8_overlap', 'Contig9', 'Contig9_GeneData', 'Contig9_TEData', 'Contig9_overlap'], identified using your supplied
                regex pattern: 'FOA_(.*?).h5', do not match the
                chromosomes in the GeneData: ['Chr_1', 'Chr_10', 'Chr_11', 'Chr_12', 'Chr_13', 'Chr_2', 'Chr_4', 'Chr_5', 'Chr_7', 'Chr_8', 'Chr_9', 'Contig1', 'Contig11', 'Contig12', 'Contig15', 'Contig17', 'Contig18', 'Contig19', 'Contig21', 'Contig22', 'Contig23', 'Contig24', 'Contig25', 'Contig26', 'Contig29', 'Contig3', 'Contig31', 'Contig32', 'Contig33', 'Contig34', 'Contig36', 'Contig38', 'Contig4', 'Contig42', 'Contig46', 'Contig49', 'Contig50', 'Contig51', 'Contig52', 'Contig54', 'Contig56', 'Contig59', 'Contig62', 'Contig65', 'Contig67', 'Contig68', 'Contig69', 'Contig7', 'Contig8', 'Contig9'].

SolayMane avatar Apr 11 '23 14:04 SolayMane