diff --git a/LDlink/LDhap.py b/LDlink/LDhap.py index 2ea42fc5..42e01884 100755 --- a/LDlink/LDhap.py +++ b/LDlink/LDhap.py @@ -134,16 +134,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/LDmatrix.py b/LDlink/LDmatrix.py index c1f23ad0..2044bf02 100755 --- a/LDlink/LDmatrix.py +++ b/LDlink/LDmatrix.py @@ -115,16 +115,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/LDpair.py b/LDlink/LDpair.py index 059a51ef..82b5c933 100755 --- a/LDlink/LDpair.py +++ b/LDlink/LDpair.py @@ -78,16 +78,16 @@ def replace_coord_rsid(db, snp): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: var_id = "rs" + ref_variants[0] return var_id diff --git a/LDlink/LDproxy.py b/LDlink/LDproxy.py index 3446d3df..7eb0c41d 100755 --- a/LDlink/LDproxy.py +++ b/LDlink/LDproxy.py @@ -90,16 +90,16 @@ def replace_coord_rsid(db, snp): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp else: var_id = "rs" + ref_variants[0] return var_id diff --git a/LDlink/SNPchip.py b/LDlink/SNPchip.py index ce5548a2..6e5420f2 100755 --- a/LDlink/SNPchip.py +++ b/LDlink/SNPchip.py @@ -135,16 +135,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/SNPclip.py b/LDlink/SNPclip.py index b18b0b92..1eea0488 100755 --- a/LDlink/SNPclip.py +++ b/LDlink/SNPclip.py @@ -123,16 +123,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/SNPcoord.py b/LDlink/SNPcoord.py index 44f6be9b..66f2843d 100755 --- a/LDlink/SNPcoord.py +++ b/LDlink/SNPcoord.py @@ -93,16 +93,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/SNPpull.py b/LDlink/SNPpull.py index b944a493..0369a95d 100755 --- a/LDlink/SNPpull.py +++ b/LDlink/SNPpull.py @@ -95,16 +95,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/SNPtip.py b/LDlink/SNPtip.py index b97e74ca..efdfc28d 100755 --- a/LDlink/SNPtip.py +++ b/LDlink/SNPtip.py @@ -93,16 +93,16 @@ def replace_coords_rsid(db, snp_lst): var_id = "rs" + ref_variants[0] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] elif len(ref_variants) == 0 and len(snp_info_lst) > 1: var_id = "rs" + snp_info_lst[0]['id'] if "warning" in output: output["warning"] = output["warning"] + \ - ". Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + ". Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: - output["warning"] = "Multiple rsIDs (" + ", ".join(ref_variants) + ") map to genomic coordinates " + snp_raw_i[0] + output["warning"] = "Multiple rsIDs (" + ", ".join(["rs" + ref_id for ref_id in ref_variants]) + ") map to genomic coordinates " + snp_raw_i[0] else: var_id = "rs" + ref_variants[0] new_snp_lst.append([var_id]) diff --git a/LDlink/news.html b/LDlink/news.html index 560fd9db..46ddbb9d 100644 --- a/LDlink/news.html +++ b/LDlink/news.html @@ -1,4 +1,4 @@ -

02/01/2019 -- New features in LDlink 3.4.0.

+

02/06/2019 -- New features in LDlink 3.4.0.