diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 71 |
1 files changed, 36 insertions, 35 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 16eaee24..434db19d 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -1356,41 +1356,42 @@ class DisplayMappingResults: yPaddingTop = yTopOffset for index, homology_dict in enumerate(self.homology): - if self.dataset.group.species == "mouse": - mm10_start = homology_dict["mm10_start"] - mm10_end = homology_dict["mm10_end"] - hg38_chr = homology_dict["hg38_chr"] - hg38_strand = homology_dict["hg38_strand"] - hg38_start = homology_dict["hg38_start"] - hg38_end = homology_dict["hg38_end"] - geneLength = (mm10_end - mm10_start) * 1000.0 - tenPercentLength = geneLength * 0.0001 - - geneStartPix = xLeftOffset + \ - plotXScale * (float(mm10_start) - startMb) - geneEndPix = xLeftOffset + plotXScale * \ - (float(mm10_end) - startMb) # at least one pixel - - if (geneEndPix < xLeftOffset): - return # this gene is not on the screen - elif (geneEndPix > xLeftOffset + plotWidth): - geneEndPix = xLeftOffset + plotWidth # clip the last in-range gene - if (geneStartPix > xLeftOffset + plotWidth): - return # we are outside the valid on-screen range, so stop drawing genes - elif (geneStartPix < xLeftOffset): - geneStartPix = xLeftOffset # clip the first in-range gene - - # color the gene based on SNP density - # found earlier, needs to be recomputed as snps are added - # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 - - myColor = BLACK - - outlineColor = myColor - fillColor = myColor - - TITLE = f"hg38: Chr {hg38_chr} from {hg38_start:.3f} to {hg38_end:.3f} Mb" - HREF = f"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr{hg38_chr}:{int(hg38_start * 1000000)}-{int(hg38_end * 1000000)}" + ref_strand = homology_dict["ref_strand"] + ref_start = homology_dict["ref_start"] + ref_end = homology_dict["ref_end"] + query_chr = homology_dict["query_chr"] + query_strand = homology_dict["query_strand"] + query_start = homology_dict["query_start"] + query_end = homology_dict["query_end"] + + geneLength = (ref_end - ref_start) * 1000.0 + tenPercentLength = geneLength * 0.0001 + + geneStartPix = xLeftOffset + \ + plotXScale * (float(ref_start) - startMb) + geneEndPix = xLeftOffset + plotXScale * \ + (float(ref_end) - startMb) # at least one pixel + + if (geneEndPix < xLeftOffset): + return # this gene is not on the screen + elif (geneEndPix > xLeftOffset + plotWidth): + geneEndPix = xLeftOffset + plotWidth # clip the last in-range gene + if (geneStartPix > xLeftOffset + plotWidth): + return # we are outside the valid on-screen range, so stop drawing genes + elif (geneStartPix < xLeftOffset): + geneStartPix = xLeftOffset # clip the first in-range gene + + # color the gene based on SNP density + # found earlier, needs to be recomputed as snps are added + # always apply colors now, even if SNP Track not checked - Zach 11/24/2010 + + myColor = BLACK + + outlineColor = myColor + fillColor = myColor + + TITLE = f"hg38: Chr {hg38_chr} from {hg38_start:.3f} to {hg38_end:.3f} Mb" + HREF = f"http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr{hg38_chr}:{int(hg38_start * 1000000)}-{int(hg38_end * 1000000)}" # Draw Genes geneYLocation = yPaddingTop + \ |