o 1wiV@s4dZddlZddlZddlZddlZddlmZ ddl m Z ddl mZddlZddlZddlZddlZddlZddlmZddlZdejd<ejdeeejdddlmZmZm Z m!Z!m"Z"m#Z#d d d Z$d!d dZ%d ddZ&d"ddZ'd#ddZ(   d$ddZ)d%ddZ*ddZ+e,dkre+dSdS)&z Generate combined figure with FIMO scans and ChromBPNet predictions. Usage: python regenerate_plot_svg.py python regenerate_plot_svg.py variant_1 thyroid_gland__ENCSR474XFV svg N)GridSpec)Pathnonez svg.fonttypevarbook)_extract_variant_sequences _plot_profile _plot_shap _plotter_shap_resolve_model_metadata _process_single_model_with_folds,c CsZt|}t|}|d}|d}||} ||} t||| | j} |} | | | fS)ap Extract sequence around variant for FIMO scanning. Parameters: ----------- chrom : str Chromosome pos : int 1-based variant position ref : str Reference allele alt : str Alternate allele genome_fa : str Path to genome FASTA window_size : int Window size around variant Returns: -------- sequence : str DNA sequence around variant (reference allele) start_pos : int Genomic start position of sequence (0-based) variant_pos_in_seq : int Position of variant within sequence (0-based) )pyfaidxFastastrsequpper) chromposrefalt genome_fa window_sizegenome pos_0based half_window seq_startseq_endsequencevariant_pos_in_seqr!regenerate_plot_svg.pyextract_sequence_for_fimo,s  r#{Gz?c stj|d}t|d}|d|d|dWdn1s#wYtj|d}ddt|d |d d||g }td d |tj|d d d} | j dkr[t d| j tj|dd} tj | sptj|d} tj | s}t d| tj| dddddddddddddddd jfd d!jDd"gd#} fd$d%| D} | rtd&| td'td(S))ao Run FIMO scan on sequence using JASPAR database. Parameters: ----------- sequence : str DNA sequence to scan sequence_name : str Name for sequence (used in FIMO output) jaspar_meme_file : str Path to JASPAR CORE database in MEME format output_dir : str Directory for FIMO output pvalue_threshold : float P-value threshold for FIMO (default: 1e-2) Returns: -------- fimo_df : pd.DataFrame FIMO results with columns: pattern_name, sequence_name, start, stop, strand, score, p-value, q-value, matched_sequence z sequence.faw> Nzfimo.txtfimoz--threshz--ocz--ozRunning FIMO:  T)capture_outputtextrz FIMO failed: zfimo.tsvz#FIMO output not found. Expected at  #)sepcomment pattern_name sequence_namestartstopstrandscorep-valueq-valuematched_sequence) z pattern namez sequence namer2r3endr4r5r6pvaluer7qvaluezmatched sequencecsi|] }|||qSr!)get.0col)column_mappingr!r" z!run_fimo_scan..columns)r0r2r3r6csg|] }|jvr|qSr!rCr=)fimo_dfr!r" rBz!run_fimo_scan..z&FIMO output missing required columns: zFound z FIMO hits)ospathjoinopenwriterprint subprocessrun returncode RuntimeErrorstderrexistsFileNotFoundErrorpdread_csvrenamerD ValueErrorlen) rr1jaspar_meme_file output_dirpvalue_threshold fasta_filef fimo_outputcmdresultfimo_tsv required_cols missing_colsr!)r@rEr" run_fimo_scanWsT     rdcCs||d}|dd||d<|dd||d<dd}|d||d <d d }|d ||d <|d}||d| k|d|k@}|S)a Process FIMO results and convert to plot coordinates. Parameters: ----------- fimo_df : pd.DataFrame FIMO results variant_pos_genomic : int Genomic position of variant (1-based) seq_start_genomic : int Genomic start position of sequence (0-based) window_size : int Window size Returns: -------- fimo_df : pd.DataFrame FIMO DataFrame with added columns: - start_rel: Start position relative to variant (variant at 0) - end_rel: End position relative to variant - color: Color based on p-value - tf_name: Cleaned TF name r r2 start_relr3end_relcSsBd|vr|d}t|dkr|ddrd|ddS|S)N_r rMA)splitrX startswithrI)r0partsr!r!r" clean_tf_names  z+process_fimo_results..clean_tf_namer0tf_namecSs4|dkrdS|dkr dS|dkrdS|dkrdSd S) Ngh㈵>navyg-C6? mediumbluegMbP? lightbluer$ lightgray gainsboror!)pvalr!r!r" assign_colorsz*process_fimo_results..assign_colorr6colorr)applycopy)rEvariant_pos_genomicseq_start_genomicrr rlrtrr!r!r"process_fimo_resultss    rzc Cs|d}|| ||gd|jddddd|j|d|ddd dd |j|d|ddd dd |d d g}i}d}d} |D]t\} } | d } | d } | d}d}tdD]3}|| }d}|D]\}\}}t||dkr||ks| |ksd}nqj|s|}| |f||<nq^|durqH|| }|j ||| d| ddddd| |d}|j ||| dddddqH|r| dt | dn| dd|jdddd d!|g|jd"d|jd#d|jd$ddS)%a Plot FIMO scan tracks. Parameters: ----------- ax : matplotlib.axes.Axes Axis for FIMO section fimo_df : pd.DataFrame FIMO DataFrame with start_rel, end_rel, tf_name, color window_size : int Window size protein_footprint : tuple (start, end) for protein footprint region variant_region : tuple (start, end) for variant region rir2rblack--r ru linestyle linewidth皙?rpalpharuzorder peachpuffrermg?rfNdF?Tg333333?ru)leftheightru edgecolorrrcenter)havafontsizerzPredicted TF-binding ElementsZ rotationlabelpadrbottomtopright)set_xlim set_xticksaxvlineaxvspan sort_valuesiterrowsrangeitemsabsbarhr+set_ylimmaxkeys set_ylabelset_xticklabelsspines set_visible)axrErprotein_footprintvariant_regionrfimo_df_sorted y_positions y_current y_spacingidxrowrmrerfy_posyy_valoverlaps existing_yexisting_start existing_endwidthmid_xr!r!r"plot_fimo_scanssf       rcCsF|D]}|j|d|ddddd|j|d|dddddqdS)z@ Add shaded regions to all panels for visual alignment. rr rrprrN)r) axes_listrrrr!r!r"add_shaded_regionsMsrBcudac :Csbtdtd|td|tdtdtj|dd} d| jvr*td| | d|k}t|d krBtd |d ||jd }|d }t|d }d|jvrdd|jvrd|d}|d}nd|jvrwd|jvrw|d}|d}ntdtd|d|d|d|tdt ||||||d\}}}tdt|dtd|d|d|t|tdt (}t ||d|||| d}t ||||d}tdt|dWd n1swYtd!t||}|d"}td#t||||||d$\}}}}td%|d&td't|||||d(| d)\}}} }!}"}#}$td*|$d+td,tjd-d.d/}%td0d1|%gd2d3d4}&td5|%|&d }'t|'||| | d6td7|%|&d1}(|dkrrt|nd })|dkr}t|nd }*|dkr|nd8}+|dkr|nd8},t|||)|*|+|,||(|$d d9 |(jd:d;d|(jd:d=d?t|(|dt|(g| | |%|&d@}-|"d j}.|#d j}/dA}0|0d@}1|d@}2|.|1|2|1|2|)}3tj|3gdBdC}4|4j|2 7_tj |4|-dD|-j!dEdFdGd1dH|-j!|)dIdFdGd1dHdJt"#t"$|3d }5dJt"%t"&|3d }6|-j'|6|5dKtj(dLdMdN|+dOdPdQ|-j)d=dRt*dSdTdUdVdW |-jdXd;d|-jdXd=d?t|-|dt|-g| | |%|&dY}7|/|1|2|1|2|*}8tj|8gdBdC}9|9j|2 7_tj |9|7dD|7j!dEdFdGd1dH|7j!|*dIdFdGd1dHdJt#t"#t"$|3d t"#t"$|8d }5dJt%t"%t"&|3d t"%t"&|8d }6|7j'|6|5dKtj(dLdMdZ|,dOdPdQ|7j)d=dRt*dSdTdUdVdW |7jd[d;d|7jd[d=d?|7j+d\d=d?t|7|dt|7g| | td]|d^|%j,||-d_d`dad.dbtdc|%S)dzN Generate combined figure with FIMO scans and ChromBPNet predictions. zP================================================================================z(Generating combined figure for variant: zModel: z" 1. Loading variant information...r,)r. variant_idz-variants_tsv must contain 'variant_id' columnrzVariant z not found in chrrrrallele1allele2zKVariants TSV must contain either 'ref'/'alt' or 'allele1'/'allele2' columnsz Variant: :u→z( 2. Extracting sequence for FIMO scan...)rz Sequence length: z bpz Genomic region: -z 3. Running FIMO scan...)r[z Found z FIMO hits in windowNz 4. Resolving model metadata... model_foldsz* 5. Extracting sequences for ChromBPNet...) input_lenz Extracted z bp sequencesz9 6. Generating ChromBPNet predictions and attributions...) n_shufflesdevicez LogFC: z.3fz 7. Creating figure layout...)ri)figsizedpir )g?r r r g333333?)figure height_ratioshspacez 8. Plotting FIMO scans...)rrrz& 9. Plotting ChromBPNet predictions...)logfc logfc_pvalzPredicted Profilesrrrr)rrr)ACGTrC)rrkrrrg?)rrgV-?gL7A`?zref ()rrrroundwhite lightgrey)boxstyle facecolorr)verticalalignmenthorizontalalignment transformsizerubboxzContrib. Scores (STRwt)rzalt (zContrib. Scores (STRmut)zRelative genomic position (bp)z 8. Saving figure to z....tight)format bbox_inchesru✓ Figure saved successfully).rLrTrUrDrWrXilocintindexr#tempfileTemporaryDirectoryrdrzr rr pltrr add_subplotrrr set_titleconfigure_shared_xaxisrcpunumpyr DataFrame logomakerLogornprmaximumminminimumrr+ transAxesdict set_xlabelsavefigri):r model_name variants_tsvmodel_paths_tsvrrY output_filerrrrr[r variants_df variant_rowrrrrrryr temp_dirrEmetadatarref_seqalt_seq ref_seq_str alt_seq_str ref_profile alt_profile ref_count alt_countref_attralt_attrrfiggsax_fimoax1 ref_length alt_length ref_label alt_labelax2 ref_attr_np alt_attr_np total_lengthrF ref_shap_plotdf_refymaxyminax3 alt_shap_plotdf_altr!r!r"generate_combined_figure\s         "         **  r0cCs:|d}|| ||gd|j|dddddS)z'Configure shared x-axis for all panels.rrrrr rN)rrr)rvariant_pos_relrrr!r!r"rsrcCsdtjdd}|jddd|jddd|jdgd d d d |jd ddd|jdddd|jdddd|jdddd|jddd|jdtddd|jdd td!d"gd#d$|jd%d td&d'gd(d$|jd)td*d+d|jd,d-d-d.gd/d0|}|js|jd1|jd2|j |_t |j|j|j |j |j |j|j|jt|jt|j|j|jd3 dS)4NzCGenerate combined figure with FIMO scans and ChromBPNet predictions) descriptionrzVariant ID (e.g., 'variant_1'))helpr z/Model name (e.g., 'thyroid_gland__ENCSR474XFV') output_format)svgpngpdfr5zOutput format (default: svg))choicesdefaultr3z--variants-tsvTzPath to variants TSV file)requiredr3z--model-paths-tsvzPath to model paths TSV filez --genome-fazb/oak/stanford/groups/akundaje/airanman/refs/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fastazPath to reference genome FASTA)r9r3z --jaspar-memez+Path to JASPAR CORE database in MEME formatz --output-filez*Output file path (default: auto-generated)z --window-sizer z)Window size around variant (default: 300))typer9r3z--protein-footprintrr|r}z+Protein footprint region (default: -40 -10))nargsr;r9r3z--variant-regionrrzVariant region (default: -5 5)z--pvalue-thresholdr$z&FIMO p-value threshold (default: 1e-2)z--devicerrz%Device for ChromBPNet (default: cuda))r9r8r3rgr) rr r r rrYr rrrr[r)argparseArgumentParser add_argumentrfloat parse_argsr rr r4r0r r r jaspar_memertuplerrr[r)parserargsr!r!r"main"sp   rF__main__)r )r$)r r{r~)r{r~)r rr{r~r$r)rr )-__doc__r=rrpandasrT matplotlibmatplotlib.pyplotpyplotrmatplotlib.patchespatchesmpatchesmatplotlib.gridspecrrrrMrrGpathlibrsysrcParamsrHinsertr__file__parentvarbook.plot.variant.profilesrrrr r r r#rdrzrrr0rrF__name__r!r!r!r"sB       + U K V  ; 6