Parsing snp result
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Entering edit mode
14 months ago
chaochao ▴ 20

I am trying to parse dbSNP results into data frame in python, I got the result as "bytes" and I wonder if there is a way to parse it into dataframe. I tried multiple xml packages (xml, lxml) but they are not able to separate the arguments in the response.content. Does anyone know how to parse the result showed below into dataframe?

Below is the script and output:

import requests
response = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=1593319917&report=XML")
print(response.content)

b'<?xml version="1.0" ?>\n<ExchangeSet xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xmlns="https://www.ncbi.nlm.nih.gov/SNP/docsum" xsi:schemaLocation="https://www.ncbi.nlm.nih.gov/SNP/docsum ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_eutils.xsd" ><DocumentSummary uid="1593319917"><SNP_ID>1593319917</SNP_ID><ALLELE_ORIGIN/><GLOBAL_MAFS><MAF><STUDY>SGDP_PRJ</STUDY><FREQ>G=0.5/1</FREQ></MAF></GLOBAL_MAFS><GLOBAL_POPULATION/><GLOBAL_SAMPLESIZE>0</GLOBAL_SAMPLESIZE><SUSPECTED/><CLINICAL_SIGNIFICANCE/><GENES><GENE_E><NAME>FLT3</NAME><GENE_ID>2322</GENE_ID></GENE_E></GENES><ACC>NC_000013.11</ACC><CHR>13</CHR><HANDLE>SGDP_PRJ</HANDLE><SPDI>NC_000013.11:28102567:G:A</SPDI><FXN_CLASS>upstream_transcript_variant</FXN_CLASS><VALIDATED>by-frequency</VALIDATED><DOCSUM>HGVS=NC_000013.11:g.28102568G>A,NC_000013.10:g.28676705G>A,NG_007066.1:g.3001C>T|SEQ=[G/A]|LEN=1|GENE=FLT3:2322</DOCSUM><TAX_ID>9606</TAX_ID><ORIG_BUILD>154</ORIG_BUILD><UPD_BUILD>154</UPD_BUILD><CREATEDATE>2020/04/27 06:19</CREATEDATE><UPDATEDATE>2020/04/27 06:19</UPDATEDATE><SS>3879653181</SS><ALLELE>R</ALLELE><SNP_CLASS>snv</SNP_CLASS><CHRPOS>13:28102568</CHRPOS><CHRPOS_PREV_ASSM>13:28676705</CHRPOS_PREV_ASSM><TEXT/><SNP_ID_SORT>1593319917</SNP_ID_SORT><CLINICAL_SORT>0</CLINICAL_SORT><CITED_SORT/><CHRPOS_SORT>0028102568</CHRPOS_SORT><MERGED_SORT>0</MERGED_SORT></DocumentSummary>\n</ExchangeSet>'

I also tried efetch using the SNP_ID but no record is found:

handle=Entrez.efetch(db="snp", id='1593319917')
snp=SeqIO.read(handle, format="gb")
print(snp)
ValueError: No records found in handle
SNP • 480 views
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Entering edit mode
10 months ago
Luis • 0

To parse your response content you first have to decode the byte-string:

record=response.content.decode("utf-8")

Then you have to clean the xml to make it compatible with xml.etree:

record=record.replace('<?xml version="1.0" ?>\n<ExchangeSet xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xmlns="https://www.ncbi.nlm.nih.gov/SNP/docsum" xsi:schemaLocation="https://www.ncbi.nlm.nih.gov/SNP/docsum ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_eutils.xsd" >','')

record=record.replace(.'</ExchangeSet>','')

In principle you could them create a xml object:

import xml.etree.ElementTree as ET
root=ET.fromstring("<root>"+record+"</root>")
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