diff --git a/tutorials/eUtils.ipynb b/tutorials/eUtils.ipynb
index 53b33a2..86a893a 100644
--- a/tutorials/eUtils.ipynb
+++ b/tutorials/eUtils.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 1,
"metadata": {
"scrolled": true
},
@@ -11,8 +11,16 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Requirement already satisfied: biopython in /srv/conda/envs/notebook/lib/python3.7/site-packages (1.74)\r\n",
- "Requirement already satisfied: numpy in /srv/conda/envs/notebook/lib/python3.7/site-packages (from biopython) (1.17.1)\r\n"
+ "Requirement already satisfied: biopython in c:\\python38\\lib\\site-packages (1.79)\n",
+ "Requirement already satisfied: numpy in c:\\python38\\lib\\site-packages (from biopython) (1.20.1)\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available.\n",
+ "You should consider upgrading via the 'C:\\Python38\\python.exe -m pip install --upgrade pip' command.\n"
]
}
],
@@ -24,7 +32,7 @@
},
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -34,7 +42,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
@@ -55,7 +63,7 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
@@ -66,7 +74,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 5,
"metadata": {},
"outputs": [
{
@@ -77,10 +85,10 @@
"RetMax : 5\n",
"RetStart : 0\n",
"QueryKey : 1\n",
- "WebEnv : NCID_1_3075896_130.14.18.97_9001_1567108675_833541832_0MetA0_S_MegaStore\n",
+ "WebEnv : MCID_61327ef47c171e289112e960\n",
"IdList : ['386571803', '118204057', '52818902', '17850737', '268']\n",
- "TranslationSet : []\n",
- "TranslationStack : [{'Term': 'LPL[All Fields]', 'Field': 'All Fields', 'Count': '21533', 'Explode': 'N'}, {'Term': 'pathogenic[Clinical_Significance]', 'Field': 'Clinical_Significance', 'Count': '70373', 'Explode': 'N'}, 'AND', {'Term': 'missense variant[Function_Class]', 'Field': 'Function_Class', 'Count': '7741037', 'Explode': 'N'}, 'AND', {'Term': '00000.0000[GLOBAL_MAF]', 'Field': 'GLOBAL_MAF', 'Count': '0', 'Explode': 'N'}, {'Term': '00000.0100[GLOBAL_MAF]', 'Field': 'GLOBAL_MAF', 'Count': '0', 'Explode': 'N'}, 'RANGE', 'GROUP', 'AND']\n",
+ "TranslationSet : [{'From': 'LPL[All Fields]', 'To': 'LPL[All Fields]'}]\n",
+ "TranslationStack : [{'Term': 'LPL[All Fields]', 'Field': 'All Fields', 'Count': '12455', 'Explode': 'N'}, {'Term': 'pathogenic[Clinical_Significance]', 'Field': 'Clinical_Significance', 'Count': '98208', 'Explode': 'N'}, 'AND', {'Term': 'missense variant[Function_Class]', 'Field': 'Function_Class', 'Count': '9628782', 'Explode': 'N'}, 'AND', {'Term': '00000.0000[GLOBAL_MAF]', 'Field': 'GLOBAL_MAF', 'Count': '0', 'Explode': 'N'}, {'Term': '00000.0100[GLOBAL_MAF]', 'Field': 'GLOBAL_MAF', 'Count': '0', 'Explode': 'N'}, 'RANGE', 'GROUP', 'AND']\n",
"QueryTranslation : LPL[All Fields] AND pathogenic[Clinical_Significance] AND missense variant[Function_Class] AND (00000.0000[GLOBAL_MAF] : 00000.0100[GLOBAL_MAF])\n"
]
}
@@ -97,7 +105,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
@@ -108,7 +116,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
@@ -133,7 +141,7 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
@@ -148,7 +156,7 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
@@ -156,19 +164,17 @@
"output_type": "stream",
"text": [
"Going to download record 1 to 2\n",
- "\n",
- "2681000GenomesG=0.0052/26ALSPACG=0.0187/72EstonianG=0.0239/107ExACG=0.0134/1622GnomADG=0.0145/455GnomAD_exomesG=0.0128/3212NorthernSwedenG=0.0283/17PAGE_STUDYG=0.0050/391TOPMEDG=0.0109/1370TWINSUKG=0.0200/740pathogenic,risk-factorLPL4023NC_000008.118DEBNICK,PERLEGEN,MGC_GENOME_DIFF,APPLERA_GI,PERLEGEN,AFFY,ILLUMINA,BCMHGSC_JDW,ENSEMBL,ILLUMINA,PAGE_STUDY,BCM-HGSC-SUB,1000GENOMES,1000GENOMES,1000GENOMES,OMICIA,ILLUMINA,OMIM-CURATED-RECORDS,1000GENOMES,NHLBI-ESP,1000GENOMES,EXOME_CHIP,CLINSEQ_SNP,ILLUMINA,ILLUMINA,ILLUMINA,EVA-GONL,1000GENOMES,EVA_GENOME_DK,EVA_FINRISK,EVA_DECODE,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,EVA_EXAC,EVA_MGP,EVA_SVP,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,JJLAB,HUMAN_LONGEVITY,TOPMED,ILLUMINA,ILLUMINA,GNOMAD,GNOMAD,GNOMAD,AFFY,AFFY,SWEGEN,ILLUMINA,ILLUMINA,CSHL,TOPMED,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,EGCUT_WGS,EVA_DECODE,ILLUMINA,ACPOP,ILLUMINA,ILLUMINA,ILLUMINA,EVA,PAGE_CC,ILLUMINAcoding_sequence_variant,missense_variantby-frequency,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NG_008855.1:g.21948A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|GENE=LPL:40239606361532000/09/19 17:022019/07/13 14:17268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551Rsnv8:19956018MergedRs=2680000000268100199560181\n",
- "1182040571000GenomesA=0.0002/1ALSPACA=0.0005/2ExACA=0.0001/16GnomADA=0.0001/2GnomAD_exomesA=0.0002/48PAGE_STUDYA=0.0002/13TOPMEDA=0.0003/32TWINSUKA=0.0003/10pathogenicLPL4023NC_000008.118OMIM-CURATED-RECORDS,NHLBI-ESP,EXOME_CHIP,ILLUMINA,ILLUMINA,1000GENOMES,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,EVA_EXAC,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,HUMAN_LONGEVITY,TOPMED,GNOMAD,GNOMAD,GNOMAD,AFFY,AFFY,SWEGEN,ILLUMINA,TOPMED,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,PAGE_CC,ILLUMINAcoding_sequence_variant,missense_variantby-frequency,by-clusterHGVS=NC_000008.11:g.19954222G>A,NC_000008.11:g.19954222G>C,NC_000008.10:g.19811733G>A,NC_000008.10:g.19811733G>C,NG_008855.2:g.57506G>A,NG_008855.2:g.57506G>C,NG_008855.1:g.20152G>A,NG_008855.1:g.20152G>C,NM_000237.3:c.644G>A,NM_000237.3:c.644G>C,NM_000237.2:c.644G>A,NM_000237.2:c.644G>C,NP_000228.1:p.Gly215Glu,NP_000228.1:p.Gly215Ala|SEQ=[G/A/C]|GENE=LPL:402396061321532010/08/10 18:392019/07/13 14:17252841577,342253778,491410889,780867932,783552866,1328915074,1620133671,1663127704,1689111495,1752723234,1917826320,1946231533,1959093860,2301287816,2470945734,2737022275,2748007694,2864092706,2985433044,2986076165,3002804416,3022826051,3555882370,3630013630,3635162172,3640869462,3644964707,3653367005,3654194858,3726520329,3744577749,3745461955,3771428668,3772954548Vsnv8:199542220118204057100199542220\n",
- "\n",
+ "b'\\n2681000GenomesG=0.005192/26ALSPACG=0.018682/72EstonianG=0.023884/107ExACG=0.013363/1622FINRISKG=0.013158/4GENOME_DKG=0.05/2GnomADG=0.013274/1862GnomAD_exomesG=0.01278/3212GoNLG=0.03006/30HapMapG=0.00565/4MGPG=0.013109/7NorthernSwedenG=0.028333/17PAGE_STUDYG=0.004968/391PRJEB36033G=0.028571/2SGDP_PRJA=0.5/1TOMMOG=0.00006/1TOPMEDG=0.011043/2923TWINSUKG=0.019957/74ALFAG=0.016273/35600pathogenic,uncertain-significance,risk-factorLPL4023NC_000008.1181000GENOMES,EVA_UK10K_TWINSUK,GNOMAD,AFFY,EVA_SVP,ACPOP,PERLEGEN,EVA_GENOME_DK,NHLBI-ESP,EXOME_CHIP,EVA,ENSEMBL,DEBNICK,EVA-GONL,TOPMED,OMICIA,TOMMO_GENOMICS,CLINSEQ_SNP,BCMHGSC_JDW,APPLERA_GI,SWEGEN,ILLUMINA,HUMAN_LONGEVITY,PAGE_CC,JJLAB,EGCUT_WGS,SGDP_PRJ,BCM-HGSC-SUB,EVA_DECODE,EVA_MGP,EVA_EXAC,PAGE_STUDY,MGC_GENOME_DIFF,OMIM-CURATED-RECORDS,EVA_UK10K_ALSPAC,CSHL,EVA_FINRISKNC_000008.11:19956017:A:Gmissense_variant,coding_sequence_variantby-frequency,by-alfa,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|LEN=1|GENE=LPL:40239606361552000/09/19 17:022021/04/27 04:06268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551,3824351410,3825737076,3869436715,3985347111,3986415474,4017379939,4778093028,5187654418Rsnv8:199560188:19813529MergedRs=2680000000268100199560181\\n1182040571000GenomesA=0.0002/1ALSPACA=0.000519/2ExACA=0.000132/16GnomADA=0.000235/33GnomAD_exomesA=0.000191/48PAGE_STUDYA=0.000165/13TOMMOA=0.000119/2TOPMEDA=0.000355/94TWINSUKA=0.00027/1ALFAA=0.000271/540uncertain-significance,pathogenicLPL4023NC_000008.118EVA,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,HUMAN_LONGEVITY,AFFY,ILLUMINA,TOMMO_GENOMICS,EVA_EXAC,TOPMED,PAGE_CC,EXOME_CHIP,1000GENOMES,OMIM-CURATED-RECORDS,SWEGEN,NHLBI-ESP,GNOMADNC_000008.11:19954221:G:A,NC_000008.11:19954221:G:Ccoding_sequence_variant,missense_variantby-frequency,by-alfa,by-clusterHGVS=NC_000008.11:g.19954222G>A,NC_000008.11:g.19954222G>C,NC_000008.10:g.19811733G>A,NC_000008.10:g.19811733G>C,NG_008855.2:g.57506G>A,NG_008855.2:g.57506G>C,NM_000237.3:c.644G>A,NM_000237.3:c.644G>C,NM_000237.2:c.644G>A,NM_000237.2:c.644G>C,NP_000228.1:p.Gly215Glu,NP_000228.1:p.Gly215Ala|SEQ=[G/A/C]|LEN=1|GENE=LPL:402396061321552010/08/10 18:392021/04/27 04:06252841577,342253778,491410889,780867932,783552866,1328915074,1620133671,1663127704,1689111495,1752723234,1917826320,1946231533,1959093860,2301287816,2470945734,2737022275,2748007694,2864092706,2985433044,2986076165,3002804416,3022826051,3555882370,3630013630,3635162172,3640869462,3644964707,3653367005,3654194858,3726520329,3744577749,3745461955,3771428668,3772954548,3824351387,3986415467,4778092540,5187654372Vsnv8:199542228:198117330118204057100199542220\\n'\n",
"Going to download record 3 to 4\n",
- "\n",
- "2681000GenomesG=0.0052/26ALSPACG=0.0187/72EstonianG=0.0239/107ExACG=0.0134/1622GnomADG=0.0145/455GnomAD_exomesG=0.0128/3212NorthernSwedenG=0.0283/17PAGE_STUDYG=0.0050/391TOPMEDG=0.0109/1370TWINSUKG=0.0200/740pathogenic,risk-factorLPL4023NC_000008.118DEBNICK,PERLEGEN,MGC_GENOME_DIFF,APPLERA_GI,PERLEGEN,AFFY,ILLUMINA,BCMHGSC_JDW,ENSEMBL,ILLUMINA,PAGE_STUDY,BCM-HGSC-SUB,1000GENOMES,1000GENOMES,1000GENOMES,OMICIA,ILLUMINA,OMIM-CURATED-RECORDS,1000GENOMES,NHLBI-ESP,1000GENOMES,EXOME_CHIP,CLINSEQ_SNP,ILLUMINA,ILLUMINA,ILLUMINA,EVA-GONL,1000GENOMES,EVA_GENOME_DK,EVA_FINRISK,EVA_DECODE,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,EVA_EXAC,EVA_MGP,EVA_SVP,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,JJLAB,HUMAN_LONGEVITY,TOPMED,ILLUMINA,ILLUMINA,GNOMAD,GNOMAD,GNOMAD,AFFY,AFFY,SWEGEN,ILLUMINA,ILLUMINA,CSHL,TOPMED,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,EGCUT_WGS,EVA_DECODE,ILLUMINA,ACPOP,ILLUMINA,ILLUMINA,ILLUMINA,EVA,PAGE_CC,ILLUMINAcoding_sequence_variant,missense_variantby-frequency,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NG_008855.1:g.21948A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|GENE=LPL:40239606361532000/09/19 17:022019/07/13 14:17268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551Rsnv8:19956018MergedRs=2680000000268100199560181\n",
- "2681000GenomesG=0.0052/26ALSPACG=0.0187/72EstonianG=0.0239/107ExACG=0.0134/1622GnomADG=0.0145/455GnomAD_exomesG=0.0128/3212NorthernSwedenG=0.0283/17PAGE_STUDYG=0.0050/391TOPMEDG=0.0109/1370TWINSUKG=0.0200/740pathogenic,risk-factorLPL4023NC_000008.118DEBNICK,PERLEGEN,MGC_GENOME_DIFF,APPLERA_GI,PERLEGEN,AFFY,ILLUMINA,BCMHGSC_JDW,ENSEMBL,ILLUMINA,PAGE_STUDY,BCM-HGSC-SUB,1000GENOMES,1000GENOMES,1000GENOMES,OMICIA,ILLUMINA,OMIM-CURATED-RECORDS,1000GENOMES,NHLBI-ESP,1000GENOMES,EXOME_CHIP,CLINSEQ_SNP,ILLUMINA,ILLUMINA,ILLUMINA,EVA-GONL,1000GENOMES,EVA_GENOME_DK,EVA_FINRISK,EVA_DECODE,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,EVA_EXAC,EVA_MGP,EVA_SVP,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,JJLAB,HUMAN_LONGEVITY,TOPMED,ILLUMINA,ILLUMINA,GNOMAD,GNOMAD,GNOMAD,AFFY,AFFY,SWEGEN,ILLUMINA,ILLUMINA,CSHL,TOPMED,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,EGCUT_WGS,EVA_DECODE,ILLUMINA,ACPOP,ILLUMINA,ILLUMINA,ILLUMINA,EVA,PAGE_CC,ILLUMINAcoding_sequence_variant,missense_variantby-frequency,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NG_008855.1:g.21948A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|GENE=LPL:40239606361532000/09/19 17:022019/07/13 14:17268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551Rsnv8:19956018MergedRs=2680000000268100199560181\n",
- "\n",
- "Going to download record 5 to 5\n",
- "\n",
- "2681000GenomesG=0.0052/26ALSPACG=0.0187/72EstonianG=0.0239/107ExACG=0.0134/1622GnomADG=0.0145/455GnomAD_exomesG=0.0128/3212NorthernSwedenG=0.0283/17PAGE_STUDYG=0.0050/391TOPMEDG=0.0109/1370TWINSUKG=0.0200/740pathogenic,risk-factorLPL4023NC_000008.118DEBNICK,PERLEGEN,MGC_GENOME_DIFF,APPLERA_GI,PERLEGEN,AFFY,ILLUMINA,BCMHGSC_JDW,ENSEMBL,ILLUMINA,PAGE_STUDY,BCM-HGSC-SUB,1000GENOMES,1000GENOMES,1000GENOMES,OMICIA,ILLUMINA,OMIM-CURATED-RECORDS,1000GENOMES,NHLBI-ESP,1000GENOMES,EXOME_CHIP,CLINSEQ_SNP,ILLUMINA,ILLUMINA,ILLUMINA,EVA-GONL,1000GENOMES,EVA_GENOME_DK,EVA_FINRISK,EVA_DECODE,EVA_UK10K_ALSPAC,EVA_UK10K_TWINSUK,EVA_EXAC,EVA_MGP,EVA_SVP,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,JJLAB,HUMAN_LONGEVITY,TOPMED,ILLUMINA,ILLUMINA,GNOMAD,GNOMAD,GNOMAD,AFFY,AFFY,SWEGEN,ILLUMINA,ILLUMINA,CSHL,TOPMED,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,ILLUMINA,EGCUT_WGS,EVA_DECODE,ILLUMINA,ACPOP,ILLUMINA,ILLUMINA,ILLUMINA,EVA,PAGE_CC,ILLUMINAcoding_sequence_variant,missense_variantby-frequency,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NG_008855.1:g.21948A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|GENE=LPL:40239606361532000/09/19 17:022019/07/13 14:17268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551Rsnv8:199560180000000268100199560180\n",
- "\n"
+ "b'\\n2681000GenomesG=0.005192/26ALSPACG=0.018682/72EstonianG=0.023884/107ExACG=0.013363/1622FINRISKG=0.013158/4GENOME_DKG=0.05/2GnomADG=0.013274/1862GnomAD_exomesG=0.01278/3212GoNLG=0.03006/30HapMapG=0.00565/4MGPG=0.013109/7NorthernSwedenG=0.028333/17PAGE_STUDYG=0.004968/391PRJEB36033G=0.028571/2SGDP_PRJA=0.5/1TOMMOG=0.00006/1TOPMEDG=0.011043/2923TWINSUKG=0.019957/74ALFAG=0.016273/35600pathogenic,uncertain-significance,risk-factorLPL4023NC_000008.1181000GENOMES,EVA_UK10K_TWINSUK,GNOMAD,AFFY,EVA_SVP,ACPOP,PERLEGEN,EVA_GENOME_DK,NHLBI-ESP,EXOME_CHIP,EVA,ENSEMBL,DEBNICK,EVA-GONL,TOPMED,OMICIA,TOMMO_GENOMICS,CLINSEQ_SNP,BCMHGSC_JDW,APPLERA_GI,SWEGEN,ILLUMINA,HUMAN_LONGEVITY,PAGE_CC,JJLAB,EGCUT_WGS,SGDP_PRJ,BCM-HGSC-SUB,EVA_DECODE,EVA_MGP,EVA_EXAC,PAGE_STUDY,MGC_GENOME_DIFF,OMIM-CURATED-RECORDS,EVA_UK10K_ALSPAC,CSHL,EVA_FINRISKNC_000008.11:19956017:A:Gmissense_variant,coding_sequence_variantby-frequency,by-alfa,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|LEN=1|GENE=LPL:40239606361552000/09/19 17:022021/04/27 04:06268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551,3824351410,3825737076,3869436715,3985347111,3986415474,4017379939,4778093028,5187654418Rsnv8:199560188:19813529MergedRs=2680000000268100199560181\\n2681000GenomesG=0.005192/26ALSPACG=0.018682/72EstonianG=0.023884/107ExACG=0.013363/1622FINRISKG=0.013158/4GENOME_DKG=0.05/2GnomADG=0.013274/1862GnomAD_exomesG=0.01278/3212GoNLG=0.03006/30HapMapG=0.00565/4MGPG=0.013109/7NorthernSwedenG=0.028333/17PAGE_STUDYG=0.004968/391PRJEB36033G=0.028571/2SGDP_PRJA=0.5/1TOMMOG=0.00006/1TOPMEDG=0.011043/2923TWINSUKG=0.019957/74ALFAG=0.016273/35600pathogenic,uncertain-significance,risk-factorLPL4023NC_000008.1181000GENOMES,EVA_UK10K_TWINSUK,GNOMAD,AFFY,EVA_SVP,ACPOP,PERLEGEN,EVA_GENOME_DK,NHLBI-ESP,EXOME_CHIP,EVA,ENSEMBL,DEBNICK,EVA-GONL,TOPMED,OMICIA,TOMMO_GENOMICS,CLINSEQ_SNP,BCMHGSC_JDW,APPLERA_GI,SWEGEN,ILLUMINA,HUMAN_LONGEVITY,PAGE_CC,JJLAB,EGCUT_WGS,SGDP_PRJ,BCM-HGSC-SUB,EVA_DECODE,EVA_MGP,EVA_EXAC,PAGE_STUDY,MGC_GENOME_DIFF,OMIM-CURATED-RECORDS,EVA_UK10K_ALSPAC,CSHL,EVA_FINRISKNC_000008.11:19956017:A:Gmissense_variant,coding_sequence_variantby-frequency,by-alfa,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|LEN=1|GENE=LPL:40239606361552000/09/19 17:022021/04/27 04:06268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551,3824351410,3825737076,3869436715,3985347111,3986415474,4017379939,4778093028,5187654418Rsnv8:199560188:19813529MergedRs=2680000000268100199560181\\n'\n",
+ "Going to download record 5 to 5\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "b'\\n2681000GenomesG=0.005192/26ALSPACG=0.018682/72EstonianG=0.023884/107ExACG=0.013363/1622FINRISKG=0.013158/4GENOME_DKG=0.05/2GnomADG=0.013274/1862GnomAD_exomesG=0.01278/3212GoNLG=0.03006/30HapMapG=0.00565/4MGPG=0.013109/7NorthernSwedenG=0.028333/17PAGE_STUDYG=0.004968/391PRJEB36033G=0.028571/2SGDP_PRJA=0.5/1TOMMOG=0.00006/1TOPMEDG=0.011043/2923TWINSUKG=0.019957/74ALFAG=0.016273/35600pathogenic,uncertain-significance,risk-factorLPL4023NC_000008.1181000GENOMES,EVA_UK10K_TWINSUK,GNOMAD,AFFY,EVA_SVP,ACPOP,PERLEGEN,EVA_GENOME_DK,NHLBI-ESP,EXOME_CHIP,EVA,ENSEMBL,DEBNICK,EVA-GONL,TOPMED,OMICIA,TOMMO_GENOMICS,CLINSEQ_SNP,BCMHGSC_JDW,APPLERA_GI,SWEGEN,ILLUMINA,HUMAN_LONGEVITY,PAGE_CC,JJLAB,EGCUT_WGS,SGDP_PRJ,BCM-HGSC-SUB,EVA_DECODE,EVA_MGP,EVA_EXAC,PAGE_STUDY,MGC_GENOME_DIFF,OMIM-CURATED-RECORDS,EVA_UK10K_ALSPAC,CSHL,EVA_FINRISKNC_000008.11:19956017:A:Gmissense_variant,coding_sequence_variantby-frequency,by-alfa,by-clusterHGVS=NC_000008.11:g.19956018A>G,NC_000008.10:g.19813529A>G,NG_008855.2:g.59302A>G,NM_000237.3:c.953A>G,NM_000237.2:c.953A>G,NP_000228.1:p.Asn318Ser|SEQ=[A/G]|LEN=1|GENE=LPL:40239606361552000/09/19 17:022021/04/27 04:06268,23712753,28505039,48420135,69043148,74819581,74905524,93851529,143320833,173427532,181341869,206439351,217321419,217397623,217418282,244238715,244291490,252841599,334734988,342253784,490960919,491410891,491921986,537115398,780867933,783552867,985272617,1328915147,1582593752,1584057346,1594862271,1620133702,1663127735,1689111573,1711194704,1713021090,1752723237,1917826322,1946231540,1946231541,1959093877,1959093878,2024980549,2301287943,2470945845,2634720445,2711132106,2737022388,2748007727,2864092854,2985433050,2986076176,3002804432,3022826073,3022826074,3348082024,3555882704,3625947308,3630013637,3630013638,3635162175,3638748368,3640869465,3643680166,3644964714,3644964715,3653367027,3653367028,3654194864,3670484468,3721555439,3726520351,3735467033,3744302894,3744577751,3745461958,3767717753,3771428683,3772954551,3824351410,3825737076,3869436715,3985347111,3986415474,4017379939,4778093028,5187654418Rsnv8:199560188:198135290000000268100199560180\\n'\n"
]
}
],
@@ -205,6 +211,114 @@
"\n"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Item \t []\n",
+ "Id \t 19923\n",
+ "PdbAcc \t 1L5J\n",
+ "PdbDescr \t Crystal Structure Of E. Coli Aconitase B\n",
+ "EC \t 4.2.1.3\n",
+ "Resolution \t 2.4\n",
+ "ExpMethod \t X-Ray Diffraction\n",
+ "PdbClass \t Lyase\n",
+ "PdbDepositDate \t 2002/03/07 00:00\n",
+ "MMDBEntryDate \t 2002/07/11 00:00\n",
+ "OrganismList \t ['Escherichia coli']\n",
+ "LigCode \t F3S|TRA\n",
+ "LigCount \t 2\n",
+ "ModProteinResCount \t 0\n",
+ "ModDNAResCount \t 0\n",
+ "ModRNAResCount \t 0\n",
+ "ProteinChainCount \t \n",
+ "DNAChainCount \t \n",
+ "RNAChainCount \t \n",
+ "\n",
+ "Item \t []\n",
+ "Id \t 19922\n",
+ "PdbAcc \t 1L5A\n",
+ "PdbDescr \t Crystal Structure Of Vibh, An Nrps Condensation Enzyme\n",
+ "EC \t \n",
+ "Resolution \t 2.55\n",
+ "ExpMethod \t X-Ray Diffraction\n",
+ "PdbClass \t Biosynthetic Protein\n",
+ "PdbDepositDate \t 2002/03/06 00:00\n",
+ "MMDBEntryDate \t 2002/07/11 00:00\n",
+ "OrganismList \t ['Vibrio cholerae']\n",
+ "LigCode \t \n",
+ "LigCount \t 0\n",
+ "ModProteinResCount \t 0\n",
+ "ModDNAResCount \t 0\n",
+ "ModRNAResCount \t 0\n",
+ "ProteinChainCount \t \n",
+ "DNAChainCount \t \n",
+ "RNAChainCount \t \n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "Entrez.email = \"dbsnp-user@nih.gov\" # provide your user email \n",
+ "Entrez.api_key = None\n",
+ "\n",
+ "# esummary handle\n",
+ "\n",
+ "eShandle = Entrez.esummary(db=\"structure\", id=\"19923,19922\")\n",
+ "\n",
+ "record = Entrez.read(eShandle)\n",
+ "for r in record:\n",
+ " for k in r.keys():\n",
+ " print(k, '\\t', r[k])\n",
+ " print('')\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "ERROR \t []\n",
+ "LinkSetDb \t [{'Link': [{'Id': '27832061'}, {'Id': '10818692'}, {'Id': '16610138'}, {'Id': '10075804'}, {'Id': '9743125'}, {'Id': '9697222'}, {'Id': '8879582'}, {'Id': '9081313'}, {'Id': '10644173'}, {'Id': '21618392'}, {'Id': '9492623'}, {'Id': '12567619'}, {'Id': '11014159'}, {'Id': '18551413'}, {'Id': '12017726'}, {'Id': '11837228'}, {'Id': '15459713'}, {'Id': '14505206'}, {'Id': '15054333'}, {'Id': '14681453'}, {'Id': '18551414'}, {'Id': '18769385'}, {'Id': '10185160'}, {'Id': '9846866'}, {'Id': '9210599'}, {'Id': '21871970'}, {'Id': '16539535'}, {'Id': '19194660'}, {'Id': '11398542'}, {'Id': '8634905'}, {'Id': '20470293'}, {'Id': '10550026'}, {'Id': '19384717'}, {'Id': '15067171'}, {'Id': '14681349'}, {'Id': '12717820'}, {'Id': '9847131'}, {'Id': '12721567'}, {'Id': '25905639'}, {'Id': '11503515'}, {'Id': '12594481'}, {'Id': '11280929'}, {'Id': '11125037'}, {'Id': '8374583'}, {'Id': '16351750'}, {'Id': '21311007'}, {'Id': '12700734'}, {'Id': '15085139'}, {'Id': '9104512'}, {'Id': '12478259'}, {'Id': '11769119'}, {'Id': '22139927'}, {'Id': '23470317'}, {'Id': '10700142'}, {'Id': '14681412'}, {'Id': '18793135'}, {'Id': '19304878'}, {'Id': '12728276'}, {'Id': '15701178'}, {'Id': '11119312'}, {'Id': '17695747'}, {'Id': '11104721'}, {'Id': '19432375'}, {'Id': '8634907'}, {'Id': '10461180'}, {'Id': '10668984'}, {'Id': '17467675'}, {'Id': '12440171'}, {'Id': '16340990'}, {'Id': '15457218'}, {'Id': '11301297'}, {'Id': '17301755'}, {'Id': '15085140'}, {'Id': '17441614'}, {'Id': '11977810'}, {'Id': '10991730'}, {'Id': '21633942'}, {'Id': '8634908'}, {'Id': '18432959'}, {'Id': '21975942'}, {'Id': '22012987'}, {'Id': '17483515'}, {'Id': '9847130'}, {'Id': '9784119'}, {'Id': '14630664'}, {'Id': '21085149'}, {'Id': '11557876'}, {'Id': '11465030'}, {'Id': '16204117'}, {'Id': '17051183'}, {'Id': '20373212'}, {'Id': '16943631'}, {'Id': '21508874'}, {'Id': '12788546'}, {'Id': '15383216'}, {'Id': '11465025'}, {'Id': '17361161'}, {'Id': '10864290'}, {'Id': '10431177'}, {'Id': '22406171'}, {'Id': '24564380'}, {'Id': '29494585'}, {'Id': '9916256'}, {'Id': '12140531'}, {'Id': '12058481'}, {'Id': '19060305'}, {'Id': '21328913'}, {'Id': '11233452'}, {'Id': '26492633'}, {'Id': '11466974'}, {'Id': '18416025'}, {'Id': '10498771'}, {'Id': '11465027'}, {'Id': '11125078'}, {'Id': '11465731'}, {'Id': '11041799'}, {'Id': '15156622'}, {'Id': '11125046'}, {'Id': '17124781'}, {'Id': '10972265'}, {'Id': '11880479'}, {'Id': '25127889'}, {'Id': '24078714'}, {'Id': '11780077'}, {'Id': '25712261'}, {'Id': '20730508'}, {'Id': '18273808'}, {'Id': '14616118'}, {'Id': '25411977'}, {'Id': '15973381'}, {'Id': '18428815'}, {'Id': '11041798'}, {'Id': '16513968'}, {'Id': '15153306'}, {'Id': '14534551'}, {'Id': '11041778'}, {'Id': '21390321'}, {'Id': '22260095'}, {'Id': '9841413'}, {'Id': '28089644'}, {'Id': '34166364'}, {'Id': '34043619'}, {'Id': '16696061'}], 'DbTo': 'pubmed', 'LinkName': 'pubmed_pubmed'}]\n",
+ "LinkSetDbHistory \t []\n",
+ "DbFrom \t pubmed\n",
+ "IdList \t ['10818692', '27832061']\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "Entrez.email = \"dbsnp-user@nih.gov\" # provide your user email \n",
+ "Entrez.api_key = None\n",
+ "\n",
+ "# elink handle\n",
+ "pmid='10818692,27832061'\n",
+ "eLhandle = Entrez.elink(dbfrom=\"pubmed\", id=pmid, linkname=\"pubmed_pubmed\")\n",
+ "record = Entrez.read(eLhandle)\n",
+ "for r in record:\n",
+ " for k in r.keys():\n",
+ " print(k, '\\t', r[k])\n",
+ " print()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -229,7 +343,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.3"
+ "version": "3.8.6"
}
},
"nbformat": 4,