diff options
| -rw-r--r-- | wqflask/wqflask/interval_analyst/GeneUtil.py | 21 |
1 files changed, 13 insertions, 8 deletions
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py index 5b28f458..a3fe1269 100644 --- a/wqflask/wqflask/interval_analyst/GeneUtil.py +++ b/wqflask/wqflask/interval_analyst/GeneUtil.py @@ -9,16 +9,21 @@ def load_homology(chr_name, start_mb, end_mb, source_file): for line in h_file: line_items = line.split() this_dict = { - "mm10_chr": line_items[2][3:], - "mm10_start": float(line_items[5])/1000000, - "mm10_end": float(line_items[6])/1000000, - "hg38_chr": line_items[7][3:], - "hg38_strand": line_items[9], - "hg38_start": float(line_items[10])/1000000, - "hg38_end": float(line_items[11])/1000000 + "ref_chr": line_items[2][3:], + "ref_strand": line_items[4], + "ref_start": float(line_items[5])/1000000, + "ref_end": float(line_items[6])/1000000, + "query_chr": line_items[7][3:], + "query_strand": line_items[9], + "query_start": float(line_items[10])/1000000, + "query_end": float(line_items[11])/1000000 } - if str(this_dict["mm10_chr"]) == str(chr_name) and this_dict["mm10_start"]>= start_mb and this_dict["mm10_end"] <= end_mb: + if str(this_dict["ref_chr"]) == str(chr_name) and + ((this_dict["ref_start"]>= start_mb and this_dict["ref_end"] <= end_mb) or + (this_dict["ref_start"] < start_mb and this_dict["ref_end"] <= end_mb) or + (this_dict["ref_start"] >= start_mb and this_dict["ref_end"] > end_mb) or + (this_dict["ref_start"] < start_mb and this_dict["ref_end"] > end_mb)): homology_list.append(this_dict) return homology_list |