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Human vs mouse synteny demo #3444

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Jan 9, 2023
Merged

Human vs mouse synteny demo #3444

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bd71cd3
[skip ci] Human vs mouse synteny
cmdcolin Jan 9, 2023
9a231d3
Optimize drawing long alignments with useCallback
cmdcolin Jan 9, 2023
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161 changes: 1 addition & 160 deletions plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,171 +2,12 @@ import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
import { openLocation } from '@jbrowse/core/util/io'
import { unzip } from '@gmod/bgzf-filehandle'
import PAFAdapter from '../PAFAdapter/PAFAdapter'
import { paf_chain2paf } from './util'

function isGzip(buf: Buffer) {
return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
}

/* adapted from chain2paf by Andrea Guarracino, license reproduced below
*
* MIT License
*
* Copyright (c) 2021 Andrea Guarracino
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/

function generate_record(
qname: string,
qstart: number,
qend: number,
qstrand: string,
tname: string,
tstart: number,
tend: number,
cigar: string,
numMatches: number,
) {
return {
qname,
qstart,
qend,
tname,
tstart,
tend,
strand: qstrand === '-' ? -1 : 1,
extra: {
numMatches,
blockLen: Math.max(qend - qstart, tend - tstart),
mappingQual: 0,
cg: cigar,
},
}
}

function paf_chain2paf(lines: string[]) {
let t_name = ''
let t_start = 0
let t_end = 0
let q_name = ''
let q_size = ''
let q_strand = ''
let q_start = 0
let q_end = 0
let num_matches = 0
let cigar = ''
const records = []
for (let i = 0; i < lines.length; i++) {
const l = lines[i]
const l_tab = l.replace(/ /g, '\t') // There are CHAIN files with space-separated fields
const l_vec = l_tab.split('\t')

if (l_vec[0] === 'chain') {
// Emit previous PAF row, if available
if (cigar) {
records.push(
generate_record(
q_name,
q_start,
q_end,
q_strand,
t_name,
t_start,
t_end,
cigar,
num_matches,
),
)
}

// Save query/target information
// score -- chain score
// tName -- chromosome (reference sequence)
// tSize -- chromosome size (reference sequence)
// tStrand -- strand (reference sequence)
// tStart -- alignment start position (reference sequence)
// tEnd -- alignment end position (reference sequence)
// qName -- chromosome (query sequence)
// qSize -- chromosome size (query sequence)
// qStrand -- strand (query sequence)
// qStart -- alignment start position (query sequence)
// qEnd -- alignment end position (query sequence)
// id -- chain ID
t_name = l_vec[2]
t_start = +l_vec[5]
t_end = +l_vec[6]
q_name = l_vec[7]
q_size = l_vec[8]
q_strand = l_vec[9]
q_start = +l_vec[10]
q_end = +l_vec[11]
if (q_strand === '-') {
const tmp = q_start
q_start = +q_size - q_end
q_end = +q_size - tmp
}

// Initialize PAF fields
num_matches = 0
cigar = ''
} else {
// size -- the size of the ungapped alignment
//
// dt -- the difference between the end of this block and the beginning
// of the next block (reference sequence)
//
// dq -- the difference between the end of this block and the beginning
// of the next block (query sequence)
const size_ungapped_alignment = +l_vec[0] || 0
const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0
const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0

if (size_ungapped_alignment !== 0) {
num_matches += +size_ungapped_alignment
cigar += size_ungapped_alignment + 'M'
}
if (diff_in_query !== 0) {
cigar += diff_in_query + 'I'
}
if (diff_in_target !== 0) {
cigar += diff_in_target + 'D'
}
}
}

// Emit last PAF row, if available
if (cigar) {
generate_record(
q_name,
q_start,
q_end,
q_strand,
t_name,
t_start,
t_end,
cigar,
num_matches,
)
}
return records
}

export default class ChainAdapter extends PAFAdapter {
async setupPre(opts?: BaseOptions) {
const loc = openLocation(this.getConf('chainLocation'), this.pluginManager)
Expand Down
159 changes: 159 additions & 0 deletions plugins/comparative-adapters/src/ChainAdapter/util.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,159 @@
/* adapted from chain2paf by Andrea Guarracino, license reproduced below
*
* MIT License
*
* Copyright (c) 2021 Andrea Guarracino
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/

function generate_record(
qname: string,
qstart: number,
qend: number,
qstrand: string,
tname: string,
tstart: number,
tend: number,
cigar: string,
numMatches: number,
) {
return {
qname,
qstart,
qend,
tname,
tstart,
tend,
strand: qstrand === '-' ? -1 : 1,
extra: {
numMatches,
blockLen: Math.max(qend - qstart, tend - tstart),
mappingQual: 0,
cg: cigar,
},
}
}

export function paf_chain2paf(lines: string[]) {
let t_name = ''
let t_start = 0
let t_end = 0
let q_name = ''
let q_size = ''
let q_strand = ''
let q_start = 0
let q_end = 0
let num_matches = 0
let cigar = ''
const records = []
for (let i = 0; i < lines.length; i++) {
const l = lines[i]
const l_tab = l.replace(/ /g, '\t') // There are CHAIN files with space-separated fields
const l_vec = l_tab.split('\t')

if (l_vec[0] === 'chain') {
// Emit previous PAF row, if available
if (cigar) {
records.push(
generate_record(
q_name,
q_start,
q_end,
q_strand,
t_name,
t_start,
t_end,
cigar,
num_matches,
),
)
}

// Save query/target information
// score -- chain score
// tName -- chromosome (reference sequence)
// tSize -- chromosome size (reference sequence)
// tStrand -- strand (reference sequence)
// tStart -- alignment start position (reference sequence)
// tEnd -- alignment end position (reference sequence)
// qName -- chromosome (query sequence)
// qSize -- chromosome size (query sequence)
// qStrand -- strand (query sequence)
// qStart -- alignment start position (query sequence)
// qEnd -- alignment end position (query sequence)
// id -- chain ID
t_name = l_vec[2]
t_start = +l_vec[5]
t_end = +l_vec[6]
q_name = l_vec[7]
q_size = l_vec[8]
q_strand = l_vec[9]
q_start = +l_vec[10]
q_end = +l_vec[11]
if (q_strand === '-') {
const tmp = q_start
q_start = +q_size - q_end
q_end = +q_size - tmp
}

// Initialize PAF fields
num_matches = 0
cigar = ''
} else {
// size -- the size of the ungapped alignment
//
// dt -- the difference between the end of this block and the beginning
// of the next block (reference sequence)
//
// dq -- the difference between the end of this block and the beginning
// of the next block (query sequence)
const size_ungapped_alignment = +l_vec[0] || 0
const diff_in_target = l_vec.length > 1 ? +l_vec[1] : 0
const diff_in_query = l_vec.length > 2 ? +l_vec[2] : 0

if (size_ungapped_alignment !== 0) {
num_matches += +size_ungapped_alignment
cigar += size_ungapped_alignment + 'M'
}
if (diff_in_query !== 0) {
cigar += diff_in_query + 'I'
}
if (diff_in_target !== 0) {
cigar += diff_in_target + 'D'
}
}
}

// Emit last PAF row, if available
if (cigar) {
generate_record(
q_name,
q_start,
q_end,
q_strand,
t_name,
t_start,
t_end,
cigar,
num_matches,
)
}
return records
}
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