I want to get all the info provided by the web-based PositionConverter to have the all the variants of all tanscripts of the gene by API. But, I found that though web-based tool is able, the API seems doesn't for all the cases.
def numberConversion(build, variant, gene=None):
...
...
if "c." in variant or "n." in variant:
result = [converter.c2chrom(variant)]
elif "g." in variant or "m." in variant:
result = converter.chrom2c(variant, "list", gene=gene)
else:
result = [""]
It seems the gene info will be passed only when variants with c. or g.?? Why? And then, why the web-based PositionConverter tool can convert "NM006941.3%28SOX10%29%3Ac.*1086*1087delTC" with all variants in transcripts of gene returned but it has "c.".
I want to get all the info provided by the web-based PositionConverter to have the all the variants of all tanscripts of the gene by API. But, I found that though web-based tool is able, the API seems doesn't for all the cases.
https://mutalyzer.nl/json/numberConversion?build=hg19&variant=NM_006941.3(SOX10):c.*1086_*1087delTC&gene=SOX10 Result: ["NC_000022.10:g.38368415_38368416delGA"]
https://mutalyzer.nl/json/numberConversion?build=hg19&variant=chr11:g.111959693G>T&gene=SDHD Result: ["NM_001276503.1:c.169+996G>T", "NM_001276504.1:c.155G>T", "NM_001276506.1:c.272G>T", "NM_003002.2:c.272G>T", "NM_003002.3:c.272G>T", "NR_077060.1:n.356G>T", "XM_005271644.1:c.272G>T", "LRG_9t1:c.272G>T"]
But, I can get all details in web-based PositionConverter https://mutalyzer.nl/position-converter?assembly_name_or_alias=GRCh37&description=NM_006941.3%28SOX10%29%3Ac.*1086_*1087delTC
https://mutalyzer.nl/position-converter?assembly_name_or_alias=GRCh37&description=chr11%3Ag.111959693G%3ET
I checked with the source code: rpc.py
def numberConversion(build, variant, gene=None): ... ... if "c." in variant or "n." in variant: result = [converter.c2chrom(variant)] elif "g." in variant or "m." in variant: result = converter.chrom2c(variant, "list", gene=gene) else: result = [""]
It seems the gene info will be passed only when variants with c. or g.?? Why? And then, why the web-based PositionConverter tool can convert "NM006941.3%28SOX10%29%3Ac.*1086*1087delTC" with all variants in transcripts of gene returned but it has "c.".
Please advise. Many thanks!