Merge pull request #44 from rust-bio/update_rust_htslib

closes #43

Cargo.toml

@@ -10,13 +10,13 @@ readme = "README.md"
 
 
 [dependencies]
-bio = "0.27"
+bio = "0.30"
 clap = { version = "2.31", features = ["yaml", "color", "suggestions"]}
 indicatif = "0.11"
 itertools = "0.6"
 log = "0.4.6"
 fern = "0.5.7"
-rust-htslib = "0.24"
+rust-htslib = "0.26"
 csv = "1.0.2"
 rustc-serialize = "0.3"
 quick-error = "1.2"

src/bam/call_consensus_reads/mod.rs

@@ -4,7 +4,7 @@ mod pipeline;
 use log::info;
 use pipeline::CallConsensusRead;
 use rust_htslib::bam;
-use rust_htslib::bam::{Header, Read};
+use rust_htslib::bam::{Format, Header, Read};
 use std::error::Error;
 
 pub fn call_consensus_reads_from_paths(
@@ -16,7 +16,11 @@ pub fn call_consensus_reads_from_paths(
     info!("Reading input files:\n    {}", bam_in);
     info!("Writing output to:\n    {}", bam_out);
     let bam_reader = bam::Reader::from_path(bam_in)?;
-    let bam_writer = bam::Writer::from_path(bam_out, &Header::from_template(bam_reader.header()))?;
+    let bam_writer = bam::Writer::from_path(
+        bam_out,
+        &Header::from_template(bam_reader.header()),
+        Format::BAM,
+    )?;
     CallConsensusRead::new(bam_reader, bam_writer, seq_dist, verbose_read_names)
         .call_consensus_reads()
 }

src/bam/call_consensus_reads/pipeline.rs

@@ -65,7 +65,7 @@ impl CallConsensusRead {
                         Some(record_pair) => {
                             //For right record save end position and duplicate group ID
                             group_end_idx
-                                .entry(record.cigar_cached().unwrap().end_pos()? - 1)
+                                .entry(record.cigar_cached().unwrap().end_pos() - 1)
                                 .or_insert_with(HashSet::new)
                                 .insert(duplicate_id.integer());
                             match record_pair {
@@ -86,7 +86,7 @@ impl CallConsensusRead {
                             if !record.is_paired() || record.is_mate_unmapped() {
                                 //If right or single record save end position and duplicate group ID
                                 group_end_idx
-                                    .entry(record.cigar_cached().unwrap().end_pos()? - 1)
+                                    .entry(record.cigar_cached().unwrap().end_pos() - 1)
                                     .or_insert_with(HashSet::new)
                                     .insert(duplicate_id.integer());
                                 record_storage.insert(
@@ -314,7 +314,7 @@ pub fn calc_consensus_complete_groups(
 }
 
 fn calc_overlap(l_rec: &bam::Record, r_rec: &bam::Record) -> Result<i32, Box<dyn Error>> {
-    let l_end_pos = l_rec.cigar_cached().unwrap().end_pos()?;
+    let l_end_pos = l_rec.cigar_cached().unwrap().end_pos();
     let r_start_pos = r_rec.pos();
     let l_softclips = count_softclips(l_rec.cigar_cached().unwrap().into_iter().rev())?;
     let r_softclips = count_softclips(r_rec.cigar_cached().unwrap().into_iter())?;

src/bcf/annotate_dgidb.rs

@@ -2,7 +2,7 @@ use itertools::Itertools;
 use regex::Regex;
 use reqwest;
 use rust_htslib::bcf;
-use rust_htslib::bcf::Read;
+use rust_htslib::bcf::{Format, Read};
 use serde::{Deserialize, Serialize};
 use std::collections::{HashMap, HashSet};
 use std::error::Error;
@@ -97,19 +97,16 @@ fn collect_genes(vcf_path: &str) -> Result<HashSet<String>, Box<dyn Error>> {
     Ok(total_genes)
 }
 
-//TODO Remove split by ',' when updating to latest htslib release
 fn extract_genes<'a>(
     rec: &'a mut bcf::Record,
 ) -> Result<Option<impl Iterator<Item = String> + 'a>, Box<dyn Error>> {
     let annotation = rec.info("ANN".as_bytes()).string()?;
     match annotation {
-        Some(transcripts) => Ok(Some(transcripts[0].split(|c| *c == b',').map(
-            |transcript| {
-                str::from_utf8(transcript.split(|c| *c == b'|').nth(3).unwrap())
-                    .unwrap()
-                    .to_owned()
-            },
-        ))),
+        Some(transcripts) => Ok(Some(transcripts.into_iter().map(|transcript| {
+            str::from_utf8(transcript.split(|c| *c == b'|').nth(3).unwrap())
+                .unwrap()
+                .to_owned()
+        }))),
         None => Ok(None),
     }
 }
@@ -122,7 +119,7 @@ fn modify_vcf_entries(
     let mut reader = bcf::Reader::from_path(vcf_path)?;
     let mut header = bcf::header::Header::from_template(reader.header());
     header.push_record(format!("##INFO=<ID={},Number=.,Type=String,Description=\"Combination of gene, drug, interaction types extracted from dgiDB. Each combination is pipe-seperated annotated as GENE|DRUG|TYPE\">", field_name).as_bytes());
-    let mut writer = bcf::Writer::from_stdout(&header, true, true)?;
+    let mut writer = bcf::Writer::from_stdout(&header, true, Format::VCF)?;
     match gene_drug_interactions_opt {
         None => {
             for result in reader.records() {
@@ -137,6 +134,7 @@ fn modify_vcf_entries(
                 writer.translate(&mut rec);
                 let genes = extract_genes(&mut rec)?.map(|genes| genes.collect_vec());
                 if let Some(mut genes) = genes {
+                    genes.sort();
                     genes.dedup();
                     let field_entries = build_dgidb_field(&gene_drug_interactions, genes)?;
                     let field_entries: Vec<&[u8]> =

src/bcf/baf.rs

@@ -8,8 +8,8 @@
 use itertools::repeat_n;
 use itertools::Itertools;
 use rust_htslib::bcf;
-use rust_htslib::bcf::Read;
-use rust_htslib::prelude::*;
+use rust_htslib::bcf::record::Numeric;
+use rust_htslib::bcf::{Format, Read};
 use std::error::Error;
 use std::f32;
 
@@ -19,7 +19,7 @@ pub fn calculate_baf() -> Result<(), Box<dyn Error>> {
     let mut header = bcf::Header::from_template(reader.header());
     header.push_record(b"##FORMAT=<ID=BAF,Number=A,Type=Float,Description=\"b-allele frequency\">");
 
-    let mut writer = bcf::Writer::from_stdout(&header, false, false)?;
+    let mut writer = bcf::Writer::from_stdout(&header, false, Format::BCF)?;
 
     for record in reader.records() {
         let mut record = record?;

src/bcf/fix_iupac_alleles.rs

@@ -1,35 +1,45 @@
 use std::error::Error;
 
-use itertools::Itertools;
 use bio::alphabets::dna::n_alphabet;
-use rust_htslib::bcf::{self, Read};
+use itertools::Itertools;
+use rust_htslib::bcf::{self, Format, Read};
 
 pub fn fix_iupac_alleles() -> Result<(), Box<dyn Error>> {
     let mut inbcf = bcf::Reader::from_stdin()?;
-    let mut outbcf = bcf::Writer::from_stdout(&bcf::Header::from_template(inbcf.header()), false, false)?;
+    let mut outbcf = bcf::Writer::from_stdout(
+        &bcf::Header::from_template(inbcf.header()),
+        false,
+        Format::BCF,
+    )?;
     let valid_alphabet = n_alphabet();
 
     for res in inbcf.records() {
         let mut rec = res?;
 
         let alleles = rec.alleles();
         if !alleles.iter().all(|allele| valid_alphabet.is_word(*allele)) {
-            let fixed = alleles.into_iter().map(|allele| {
-                let fixed = allele.into_iter().map(|base| {
-                    if valid_alphabet.is_word(&[*base]) {
-                        *base
-                    } else {
-                        b'N'
-                    }
-                }).collect_vec();
-                fixed
-            }).collect_vec();
+            let fixed = alleles
+                .into_iter()
+                .map(|allele| {
+                    let fixed = allele
+                        .into_iter()
+                        .map(|base| {
+                            if valid_alphabet.is_word(&[*base]) {
+                                *base
+                            } else {
+                                b'N'
+                            }
+                        })
+                        .collect_vec();
+                    fixed
+                })
+                .collect_vec();
 
             rec.set_alleles(&fixed.iter().map(|allele| allele.as_slice()).collect_vec())?;
         }
-        
+
         outbcf.write(&rec)?;
     }
 
     Ok(())
-}
+}

src/bcf/match_variants.rs

@@ -13,7 +13,7 @@ use itertools::Itertools;
 use log::{info, warn};
 use quick_error::quick_error;
 use rust_htslib::bcf;
-use rust_htslib::bcf::Read;
+use rust_htslib::bcf::{Format, Read};
 use std::collections::{btree_map, BTreeMap, HashMap};
 use std::error::Error;
 use std::str;
@@ -29,12 +29,11 @@ impl VarIndex {
         let mut i = 0;
         let mut rec = reader.empty_record();
         loop {
-            if let Err(e) = reader.read(&mut rec) {
-                if e.is_eof() {
-                    break;
-                }
-                return Err(Box::new(e));
-            }
+            match reader.read(&mut rec) {
+                Ok(true) => (),
+                Ok(false) => break,
+                Err(e) => return Err(Box::new(e)),
+            };
             if let Some(rid) = rec.rid() {
                 let chrom = reader.header().rid2name(rid)?;
                 let recs = inner.entry(chrom.to_owned()).or_insert(BTreeMap::new());
@@ -74,18 +73,17 @@ pub fn match_variants(
         alternative allele separately). For indels, matching is fuzzy: distance of centres <= {}, difference of \
         lengths <= {}\">", max_dist, max_len_diff).as_bytes()
     );
-    let mut outbcf = bcf::Writer::from_path(&"-", &header, false, false)?;
+    let mut outbcf = bcf::Writer::from_path(&"-", &header, false, Format::BCF)?;
     let index = VarIndex::new(bcf::Reader::from_path(matchbcf)?, max_dist)?;
 
     let mut rec = inbcf.empty_record();
     let mut i = 0;
     loop {
-        if let Err(e) = inbcf.read(&mut rec) {
-            if e.is_eof() {
-                break;
-            }
-            return Err(Box::new(e));
-        }
+        match inbcf.read(&mut rec) {
+            Ok(true) => (),
+            Ok(false) => break,
+            Err(e) => return Err(Box::new(e)),
+        };
         outbcf.translate(&mut rec);
 
         if let Some(rid) = rec.rid() {

src/bcf/mod.rs

@@ -1,6 +1,6 @@
 //! Tools that work on VCF and BCF files.
 pub mod annotate_dgidb;
 pub mod baf;
+pub mod fix_iupac_alleles;
 pub mod match_variants;
 pub mod to_txt;
-pub mod fix_iupac_alleles;

src/bcf/to_txt.rs

@@ -108,14 +108,11 @@ pub fn to_txt(
     writer.newline()?;
     let mut rec = reader.empty_record();
     loop {
-        if let Err(e) = reader.read(&mut rec) {
-            if e.is_eof() {
-                break;
-            } else {
-                return Err(Box::new(e));
-            }
-        }
-
+        match reader.read(&mut rec) {
+            Ok(true) => (),
+            Ok(false) => break,
+            Err(e) => return Err(Box::new(e)),
+        };
         let alleles = rec
             .alleles()
             .into_iter()

tests/expected/annotate_dgidb_test.vcf

@@ -60,4 +60,4 @@
 ##INFO=<ID=dbNSFP_M_CAP_score,Number=.,Type=Float,Description="Field 'M-CAP_score' from dbNSFP">
 ##INFO=<ID=dgiDB_drugs,Number=.,Type=String,Description="Combination of gene, drug, interaction types extracted from dgiDB. Each combination is pipe-seperated annotated as GENE|DRUG|TYPE">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal	tumor
-8	27461737	.	C	G	.	.	SVLEN=.;PROB_SOMATIC_NORMAL=18.3288;PROB_ABSENT=987.672;PROB_GERMLINE_HET=349.144;PROB_ARTIFACT=272.885;PROB_SOMATIC_TUMOR_MEDIUM=0.168458;PROB_SOMATIC_TUMOR_HIGH=16.3168;PROB_SOMATIC_TUMOR_LOW=59.5167;PROB_GERMLINE_HOM=5489.1;ANN=G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000240132.7|protein_coding|7/7|c.1437G>C|p.Lys479Asn|1601/1735|1437/1545|479/514||,G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000407991.2|protein_coding|7/7|c.1482G>C|p.Lys494Asn|2091/4067|1482/1590|494/529||,G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000520933.7|protein_coding|7/7|c.1416G>C|p.Lys472Asn|1858/2497|1416/1524|472/507||,G|3_prime_UTR_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000523695.5|nonsense_mediated_decay|7/7|c.*884G>C|||||2108|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000346049.9|protein_coding||c.*3228C>G|||||2351|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000397501.5|protein_coding||c.*3228C>G|||||2347|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000517339.5|protein_coding||c.*3228C>G|||||2351|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000522245.1|retained_intron||n.*3263C>G|||||3263|,G|downstream_gene_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000522008.1|retained_intron||n.*1891G>C|||||1891|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000420218.3|protein_coding||c.*3228C>G|||||2346|,G|downstream_gene_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000637241.1|nonsense_mediated_decay||c.*7916G>C|||||1654|,G|non_coding_transcript_exon_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000520600.1|retained_intron|2/2|n.307G>C||||||;dbNSFP_DEOGEN2_score=0.805964,.,.;dbNSFP_Ensembl_proteinid=ENSP00000385026,ENSP00000429616,ENSP00000240132;dbNSFP_Ensembl_transcriptid=ENST00000407991,ENST00000520933,ENST00000240132;dbNSFP_FATHMM_score=-0.7,.,-0.7;dbNSFP_LRT_score=0;dbNSFP_M_CAP_score=0.225545;dbNSFP_MPC_score=0.77049,.,.;dbNSFP_MVP_score=0.925048,0.925048,0.925048;dbNSFP_MetaLR_score=0.5717;dbNSFP_MetaSVM_score=0.1915;dbNSFP_MutPred_score=0.803;dbNSFP_MutationAssessor_score=3.385,.,.;dbNSFP_MutationTaster_score=0.999992,0.999992,0.999992;dbNSFP_PROVEAN_score=-4.7,.,-4.7;dbNSFP_Polyphen2_HDIV_score=0.972,.,.;dbNSFP_Polyphen2_HVAR_score=0.968,.,.;dbNSFP_PrimateAI_score=0.582399;dbNSFP_REVEL_score=0.629;dbNSFP_SIFT4G_score=0.011,0.01,0.01;dbNSFP_SIFT_score=0.001,.,0;dbNSFP_Uniprot_acc=Q15822,A0A0X1KG79,Q15822-2;dbNSFP_Uniprot_entry=ACHA2_HUMAN,A0A0X1KG79_HUMAN,ACHA2_HUMAN;dbNSFP_VEST4_score=0.431,0.426,0.641;dgiDB_drugs=CHRNA2|METOCURINE IODIDE|antagonist,CHRNA2|GALLAMINE TRIETHIODIDE|antagonist,CHRNA2|MECAMYLAMINE HYDROCHLORIDE|inhibitor,CHRNA2|PROCAINE|antagonist,CHRNA2|ATRACURIUM BESYLATE|inhibitor,CHRNA2|DOXACURIUM CHLORIDE|antagonist,CHRNA2|TUBOCURARINE|antagonist,CHRNA2|MIVACURIUM|antagonist,CHRNA2|DECAMETHONIUM|antagonist,CHRNA2|DECAMETHONIUM|partial agonist,CHRNA2|METOCURINE|antagonist,CHRNA2|PIPECURONIUM|antagonist,CHRNA2|EPIBATIDINE|agonist,CHRNA2|CP-601927|agonist,CHRNA2|HEXAMETHONIUM|channel blocker,CHRNA2|ATRACURIUM|.,CHRNA2|CISATRACURIUM BESYLATE|.,CHRNA2|DOXACURIUM|.,CHRNA2|CARBACHOL|antagonist,CHRNA2|ROCURONIUM|antagonist,CHRNA2|PANCURONIUM|.,CHRNA2|VECURONIUM|antagonist,CHRNA2|GANTACURIUM|.,CHRNA2|NICOTINE|.,CHRNA2|BIPERIDEN|.,CHRNA2|LEVALLORPHAN|antagonist,PTK2B|LEFLUNOMIDE|antagonist,PTK2B|GENISTEIN|.,PTK2B|CHEMBL509485|.,PTK2B|ALOISINE|inhibitor,PTK2B|CHEMBL458997|inhibitor,PTK2B|PF-562271|inhibitor,PTK2B|RUXOLITINIB PHOSPHATE|inhibitor,PTK2B|PIBOSEROD|inhibitor,PTK2B|DEFACTINIB|inhibitor,CHRNA2|METOCURINE IODIDE|antagonist,CHRNA2|GALLAMINE TRIETHIODIDE|antagonist,CHRNA2|MECAMYLAMINE HYDROCHLORIDE|inhibitor,CHRNA2|PROCAINE|antagonist,CHRNA2|ATRACURIUM BESYLATE|inhibitor,CHRNA2|DOXACURIUM CHLORIDE|antagonist,CHRNA2|TUBOCURARINE|antagonist,CHRNA2|MIVACURIUM|antagonist,CHRNA2|DECAMETHONIUM|antagonist,CHRNA2|DECAMETHONIUM|partial agonist,CHRNA2|METOCURINE|antagonist,CHRNA2|PIPECURONIUM|antagonist,CHRNA2|EPIBATIDINE|agonist,CHRNA2|CP-601927|agonist,CHRNA2|HEXAMETHONIUM|channel blocker,CHRNA2|ATRACURIUM|.,CHRNA2|CISATRACURIUM BESYLATE|.,CHRNA2|DOXACURIUM|.,CHRNA2|CARBACHOL|antagonist,CHRNA2|ROCURONIUM|antagonist,CHRNA2|PANCURONIUM|.,CHRNA2|VECURONIUM|antagonist,CHRNA2|GANTACURIUM|.,CHRNA2|NICOTINE|.,CHRNA2|BIPERIDEN|.,CHRNA2|LEVALLORPHAN|antagonist,PTK2B|LEFLUNOMIDE|antagonist,PTK2B|GENISTEIN|.,PTK2B|CHEMBL509485|.,PTK2B|ALOISINE|inhibitor,PTK2B|CHEMBL458997|inhibitor,PTK2B|PF-562271|inhibitor,PTK2B|RUXOLITINIB PHOSPHATE|inhibitor,PTK2B|PIBOSEROD|inhibitor,PTK2B|DEFACTINIB|inhibitor,CHRNA2|METOCURINE IODIDE|antagonist,CHRNA2|GALLAMINE TRIETHIODIDE|antagonist,CHRNA2|MECAMYLAMINE HYDROCHLORIDE|inhibitor,CHRNA2|PROCAINE|antagonist,CHRNA2|ATRACURIUM BESYLATE|inhibitor,CHRNA2|DOXACURIUM CHLORIDE|antagonist,CHRNA2|TUBOCURARINE|antagonist,CHRNA2|MIVACURIUM|antagonist,CHRNA2|DECAMETHONIUM|antagonist,CHRNA2|DECAMETHONIUM|partial agonist,CHRNA2|METOCURINE|antagonist,CHRNA2|PIPECURONIUM|antagonist,CHRNA2|EPIBATIDINE|agonist,CHRNA2|CP-601927|agonist,CHRNA2|HEXAMETHONIUM|channel blocker,CHRNA2|ATRACURIUM|.,CHRNA2|CISATRACURIUM BESYLATE|.,CHRNA2|DOXACURIUM|.,CHRNA2|CARBACHOL|antagonist,CHRNA2|ROCURONIUM|antagonist,CHRNA2|PANCURONIUM|.,CHRNA2|VECURONIUM|antagonist,CHRNA2|GANTACURIUM|.,CHRNA2|NICOTINE|.,CHRNA2|BIPERIDEN|.,CHRNA2|LEVALLORPHAN|antagonist	DP:AF:OBS:SB	116:0:83N-33N+:.	145:0.227034:91N-23V-21N+10V+:.
+8	27461737	.	C	G	.	.	SVLEN=.;PROB_SOMATIC_NORMAL=18.3288;PROB_ABSENT=987.672;PROB_GERMLINE_HET=349.144;PROB_ARTIFACT=272.885;PROB_SOMATIC_TUMOR_MEDIUM=0.168458;PROB_SOMATIC_TUMOR_HIGH=16.3168;PROB_SOMATIC_TUMOR_LOW=59.5167;PROB_GERMLINE_HOM=5489.1;ANN=G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000240132.7|protein_coding|7/7|c.1437G>C|p.Lys479Asn|1601/1735|1437/1545|479/514||,G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000407991.2|protein_coding|7/7|c.1482G>C|p.Lys494Asn|2091/4067|1482/1590|494/529||,G|missense_variant|MODERATE|CHRNA2|ENSG00000120903|transcript|ENST00000520933.7|protein_coding|7/7|c.1416G>C|p.Lys472Asn|1858/2497|1416/1524|472/507||,G|3_prime_UTR_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000523695.5|nonsense_mediated_decay|7/7|c.*884G>C|||||2108|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000346049.9|protein_coding||c.*3228C>G|||||2351|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000397501.5|protein_coding||c.*3228C>G|||||2347|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000517339.5|protein_coding||c.*3228C>G|||||2351|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000522245.1|retained_intron||n.*3263C>G|||||3263|,G|downstream_gene_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000522008.1|retained_intron||n.*1891G>C|||||1891|,G|downstream_gene_variant|MODIFIER|PTK2B|ENSG00000120899|transcript|ENST00000420218.3|protein_coding||c.*3228C>G|||||2346|,G|downstream_gene_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000637241.1|nonsense_mediated_decay||c.*7916G>C|||||1654|,G|non_coding_transcript_exon_variant|MODIFIER|CHRNA2|ENSG00000120903|transcript|ENST00000520600.1|retained_intron|2/2|n.307G>C||||||;dbNSFP_DEOGEN2_score=0.805964,.,.;dbNSFP_Ensembl_proteinid=ENSP00000385026,ENSP00000429616,ENSP00000240132;dbNSFP_Ensembl_transcriptid=ENST00000407991,ENST00000520933,ENST00000240132;dbNSFP_FATHMM_score=-0.7,.,-0.7;dbNSFP_LRT_score=0;dbNSFP_M_CAP_score=0.225545;dbNSFP_MPC_score=0.77049,.,.;dbNSFP_MVP_score=0.925048,0.925048,0.925048;dbNSFP_MetaLR_score=0.5717;dbNSFP_MetaSVM_score=0.1915;dbNSFP_MutPred_score=0.803;dbNSFP_MutationAssessor_score=3.385,.,.;dbNSFP_MutationTaster_score=0.999992,0.999992,0.999992;dbNSFP_PROVEAN_score=-4.7,.,-4.7;dbNSFP_Polyphen2_HDIV_score=0.972,.,.;dbNSFP_Polyphen2_HVAR_score=0.968,.,.;dbNSFP_PrimateAI_score=0.582399;dbNSFP_REVEL_score=0.629;dbNSFP_SIFT4G_score=0.011,0.01,0.01;dbNSFP_SIFT_score=0.001,.,0;dbNSFP_Uniprot_acc=Q15822,A0A0X1KG79,Q15822-2;dbNSFP_Uniprot_entry=ACHA2_HUMAN,A0A0X1KG79_HUMAN,ACHA2_HUMAN;dbNSFP_VEST4_score=0.431,0.426,0.641;dgiDB_drugs=CHRNA2|METOCURINE IODIDE|antagonist,CHRNA2|GALLAMINE TRIETHIODIDE|antagonist,CHRNA2|MECAMYLAMINE HYDROCHLORIDE|inhibitor,CHRNA2|PROCAINE|antagonist,CHRNA2|ATRACURIUM BESYLATE|inhibitor,CHRNA2|DOXACURIUM CHLORIDE|antagonist,CHRNA2|TUBOCURARINE|antagonist,CHRNA2|MIVACURIUM|antagonist,CHRNA2|DECAMETHONIUM|antagonist,CHRNA2|DECAMETHONIUM|partial agonist,CHRNA2|METOCURINE|antagonist,CHRNA2|PIPECURONIUM|antagonist,CHRNA2|EPIBATIDINE|agonist,CHRNA2|CP-601927|agonist,CHRNA2|HEXAMETHONIUM|channel blocker,CHRNA2|ATRACURIUM|.,CHRNA2|CISATRACURIUM BESYLATE|.,CHRNA2|DOXACURIUM|.,CHRNA2|CARBACHOL|antagonist,CHRNA2|ROCURONIUM|antagonist,CHRNA2|PANCURONIUM|.,CHRNA2|VECURONIUM|antagonist,CHRNA2|GANTACURIUM|.,CHRNA2|NICOTINE|.,CHRNA2|BIPERIDEN|.,CHRNA2|LEVALLORPHAN|antagonist,PTK2B|LEFLUNOMIDE|antagonist,PTK2B|GENISTEIN|.,PTK2B|CHEMBL509485|.,PTK2B|ALOISINE|inhibitor,PTK2B|CHEMBL458997|inhibitor,PTK2B|PF-562271|inhibitor,PTK2B|RUXOLITINIB PHOSPHATE|inhibitor,PTK2B|PIBOSEROD|inhibitor,PTK2B|DEFACTINIB|inhibitor	DP:AF:OBS:SB	116:0:83N-33N+:.	145:0.227034:91N-23V-21N+10V+:.