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Merge pull request #40 from CBIIT/LDlink_3.4.0
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prepend RS in front of refSNP IDs in warning messages
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@kvnjng
kvnjng authored Feb 4, 2019
2 parents bb4e837 + 4209e5a commit 23dcb81
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Showing 10 changed files with 37 additions and 37 deletions.
8 changes: 4 additions & 4 deletions LDlink/LDhap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/LDmatrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/LDpair.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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8 changes: 4 additions & 4 deletions LDlink/LDproxy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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8 changes: 4 additions & 4 deletions LDlink/SNPchip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/SNPclip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/SNPcoord.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/SNPpull.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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8 changes: 4 additions & 4 deletions LDlink/SNPtip.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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])
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2 changes: 1 addition & 1 deletion LDlink/news.html
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<p><b>02/01/2019</b> -- New features in <b>LDlink 3.4.0</b>.</p>
<p><b>02/06/2019</b> -- New features in <b>LDlink 3.4.0</b>.</p>
<ul>
<li>Correct dbsnp positions for delins, ins, and del type variants.</li>
<li>Improve query performance from genomic coordinate and rsid inputs.</li>
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