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A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution.

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The authors' code

Python · 153 lines · 7.5 KB · GPL-3.0

  1. #!/usr/bin/env python
  2. # -- coding:utf-8 --
  3. # Last-modified: 24 Jan 2020 12:19:13 PM
  4. #
  5. # Module/Scripts Description
  6. #
  7. # Copyright (c) 2020 Rowan Unversity
  8. #
  9. # This code is free software; you can redistribute it and/or modify it
  10. # under the terms of the BSD License (see the file COPYING included with
  11. # the distribution).
  12. #
  13. # @version: 2.0.0
  14. # @design: Yong Chen <[email hidden]>
  15. # @implementation: Yunfei Wang <[email hidden]>
  16. # @corresponding author: Yong Chen <[email hidden]>
  18. # ------------------------------------
  19. # python modules
  20. # ------------------------------------
  22. import os
  23. import sys
  24. import pandas
  25. import argparse
  28. import maxim
  30. # ------------------------------------
  31. # constants
  32. # ------------------------------------
  34. # ------------------------------------
  35. # Misc functions
  36. # ------------------------------------
  38. def argParser():
  39. ''' Parse arguments. '''
  40. p=argparse.ArgumentParser(description='MAXIM is a model-based analysis and pipeline of dCas9 Capture-3C-Seq data of multiplexed version. It uses multiplescale Bayesian models for the significance calling of chromatin interactions. It oprovides a versatile and flexible pipeline to analyze the dCas9 Capture-3C-Seq data V2.0 from raw sequencing reads to chromatin loops. MAXIM integrates all steps required for the data analysis, and it supports the multiplexed version that uses batchs of multiple targets (sgRNAs) in one experiments.',add_help=False,epilog='dependency numpy, scipy, pandas, pysam, statsmodels')
  42. pr = p.add_argument_group('Required')
  43. pr.add_argument("-x","--genome",dest="genome",type=str,metavar="hg38", required=True, help="Bowtie2 built genome.")
  44. pr.add_argument("-1",dest="fq1",type=str,metavar='sample_R1.fastq.gz',nargs="+",required=True,help="Read 1 fastq file. Can be gzip(.gz) or bzip2(.bz2) compressed.")
  45. pr.add_argument("-2",dest="fq2",type=str,metavar='sample_R2.fastq.gz',nargs="+",required=True,help="Read 2 fastq file. Can be gzip(.gz) or bzip2(.bz2) compressed.")
  46. pr.add_argument("--prefix",dest="prefix",type=str,metavar='prefix',required=True,help="Prefix of result files.")
  48. po = p.add_argument_group('Optional')
  49. po.add_argument("--bait",dest="bait",type=str,metavar="chr11:5305934",default="chr11:5305934",help="Bait genomic locus. [Default=\"chr11:5305934\"]")
  50. po.add_argument("--extendsize",dest="extendsize",type=int,metavar="100000",default=100000,help="Length to be extended from bait regions. [Defaut=100000]")
  51. po.add_argument("--readlen",dest="readlen",type=int,metavar="36",default=36,help="Read length. [Default=36]")
  52. po.add_argument("--seed",dest="seed",type=int,metavar="1024",default=1024,help="Seed to generate random values. [Default=1024].")
  53. po.add_argument("--smooth-window",dest="smooth_window",type=int,metavar="100",default=100,help="Smooth window for peak size inference. [Default=100].")
  54. po.add_argument("--peakstart", dest="peakstart", type=int, metavar=5305834, default=0, help="User defined peak start. Used together with '--peakend'.")
  55. po.add_argument("--peakend", dest="peakend", type=int, metavar=5306034, default=0, help="User defined peak end. Used together with '--peakend'.")
  56. po.add_argument("--nperm",dest="nperm",type=int,metavar="10000",default=10000,help="Number of permutatons. [Default=10000].")
  57. po.add_argument("-w",dest="wdir",type=str,metavar='"."',default=".",help="Working directory. [Default=\".\"].")
  58. po.add_argument("-p",dest='proc',type=int,metavar='10',default=10,help="Number of processes. [Default=10]")
  59. if len(sys.argv)==1:
  60. sys.exit(p.print_help())
  61. args = p.parse_args()
  62. return args
  64. # ------------------------------------
  65. # Classes
  66. # ------------------------------------
  68. # ------------------------------------
  69. # Main
  70. # ------------------------------------
  72. if __name__=="__main__":
  73. args = argParser()
  74. # check parameters
  75. peaksize = None
  76. if args.peakstart!=-1 and args.peakend!=-1:
  77. peaksize = args.peakend - args.peakstart
  78. maxim.Utils.touchtime("Use user defined peak size.")
  79. elif args.peakstart!=-1 or args.peakend!=-1:
  80. maxim.Utils.touchtime("ERROR: both '--peakstart' and '--peakend' should be provided.")
  82. # Mapping reads to genome
  83. if "-" in args.bait:
  84. start, end = args.bait.split(":")[1].split('-')
  85. args.bait = "{}:{}".format(args.bait.split(":")[0],round((int(start)+int(end))/2))
  86. mappingdir = args.wdir+"/010ReadMapping"
  87. fq1, fq2 = ",".join(args.fq1), ",".join(args.fq2)
  88. mappingdir = maxim.Utils.touchdir(mappingdir)
  90. # 1st round of mapping
  91. maxim.Utils.touchtime("FIRST ROUND OF MAPPING ...")
  92. maxim.Utils.touchtime("MAPPING READ 1 ...")
  93. maxim.Algorithms.bowtie2_SE(args.genome,fq1,args.prefix+"_R1",proc=args.proc,wdir=mappingdir,min_qual=30)
  94. maxim.Utils.touchtime("MAPPING READ 2 ...")
  95. maxim.Algorithms.bowtie2_SE(args.genome,fq2,args.prefix+"_R2",proc=args.proc,wdir=mappingdir,min_qual=30)
  96. maxim.Utils.touchtime()
  98. # Split the reads by GATC sites and take the larger one
  99. maxim.Utils.touchtime("Split read by GATC sites ...")
  100. maxim.Algorithms.ParseGATCSites("{0}/{1}_R1_un.fastq.gz".format(mappingdir,args.prefix),"{0}/{1}_R1_split.fastq.gz".format(mappingdir,args.prefix))
  101. maxim.Algorithms.ParseGATCSites("{0}/{1}_R2_un.fastq.gz".format(mappingdir,args.prefix),"{0}/{1}_R2_split.fastq.gz".format(mappingdir,args.prefix))
  102. maxim.Utils.touchtime()
  104. # 2nd round of mapping
  105. maxim.Utils.touchtime("SECOND ROUND OF MAPPING ...")
  106. maxim.Utils.touchtime("MAPPING READ 1 ...")
  107. maxim.Algorithms.bowtie2_SE(args.genome,"{0}/{1}_R1_split.fastq.gz".format(mappingdir,args.prefix),args.prefix+"_R1_remap",min_qual=30,proc=args.proc,wdir=mappingdir)
  108. maxim.Utils.touchtime("MAPPING READ 2 ...")
  109. maxim.Algorithms.bowtie2_SE(args.genome,"{0}/{1}_R2_split.fastq.gz".format(mappingdir,args.prefix),args.prefix+"_R2_remap",min_qual=30,proc=args.proc,wdir=mappingdir)
  110. maxim.Utils.touchtime()
  112. # Fix mate pairs
  113. maxim.Utils.touchtime("Merge bam files and fix mate pairs ...")
  114. bams = [mappingdir+args.prefix+f for f in ["_R1.bam", "_R2.bam", "_R1_remap.bam", "_R2_remap.bam"]]
  115. tbffile = maxim.Algorithms.FixMatePairs(bams,mappingdir+args.prefix,args.proc)
  116. maxim.Utils.touchtime()
  118. # Infer peak characteristics from the bait region
  119. plotdir = args.wdir+"/020Plotting"
  120. plotdir = maxim.Utils.touchdir(plotdir)
  121. maxim.Utils.touchtime("Draw bait figures ...")
  122. tbf = maxim.TabixFile(tbffile,peaksize)
  123. tbf.setChromSizes(bams[0])
  124. tbf.BaitStatsPlot(args.bait,
  125. plotdir+args.prefix+"_stats.pdf",
  126. extendsize=args.extendsize,
  127. readlen=args.readlen,
  128. smooth_window=args.smooth_window)
  129. maxim.Utils.touchtime()
  131. # Calculate intra- and inter-chrom interactions
  132. modeldir = args.wdir+"/030Model"
  133. modeldir = maxim.Utils.touchdir(modeldir)
  134. maxim.Utils.touchtime("Permutation on intra-chromosomal interactions ...")
  135. ns, ps = tbf.GetIntraChromLinks(nperm=args.nperm)
  136. #for n,p in zip(ns,ps):
  137. # print n,p
  138. maxim.Utils.touchtime("Permutation on inter-chromosomal interactions ...")
  139. n, p = tbf.GetInterChromLinks(nperm=args.nperm)
  141. #print n, p
  142. maxim.Utils.touchtime()
  144. # Calculate p values for intra- and inter-chrom interactions.
  145. maxim.Utils.touchtime("Calculate p values ...")
  146. tbf.InferBaitPval(modeldir+args.prefix)
  147. maxim.Utils.touchtime()
  149. # Ending
  150. maxim.Utils.touchtime("RunMAXIM finished successfully. Thank you for using MAXIM!")

runMAXIM.py at commit df92e8d, under GPL-3.0 · at the source

Overview

Authors: Jinhao Liu1, Zihang Yin2, Yonglin Peng3, Shuang Cui2, Bo Shi1, Xinrui Jiang1, Ziyi Yang4, Sijie Gu1, Yude Lin1, Lingfeng Xu1, Zhen Xu1, Xuankai Wang1, Tienan Chen1, Wei Zhang1, Shaojiao Wang1, Zhiwei Xiao1, Zhibo Huang1, Rujiang Zhou1, Zhengju Yao1, Xiaodong Zhao3, Ya Guo2, Shuhua Xu4, Weidong Li5, Xizhi Guo1
ORCID iDs: Zhibo Huang
  1. Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University,Shanghai, 200240 China
  2. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University,Shanghai, China
  3. Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University,Shanghai, China
  4. State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University,Shanghai, China
  5. Center for Brain Health and Brain Technology, Global Institute of Future Technology, Shanghai Jiao Tong University,Shanghai, China
Institutions: Shanghai Jiao Tong University (China); Fudan University (China)
Journal: Genome biology, volume 27, issue 1, article 266
Dates: received 28 October 2025; accepted 24 April 2026; published online 4 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s13059-026-04098-8 · PMID 42071237 · PMCID PMC13501865 · OpenAlex W7160027641
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), non-human primate (organism), developmental (subfield)
Methods: Connectivity, Statistics, Spectral & time-frequency
Keywords: FOXP2, LINE-1, Positive selection, Primate, Neural stem cells, Long-range chromatin interaction, Enhancer
MeSH: Cell Differentiation*, Evolution, Molecular*, Forkhead Transcription Factors*, Long Interspersed Nucleotide Elements*, Neurogenesis*, Neurons*, Animals, Chromatin, Humans, Neural Stem Cells, Pan troglodytes, Primates (* major topic)
Topic: Chromosomal and Genetic Variations (Plant Science, Agricultural and Biological Sciences), according to OpenAlex
Funding: Shanghai Science and Technology Commission Program (25JS2810100, 23JS1410100); “111” Program of Higher Education Discipline Innovation and Shanghai Municipal Science and Technology Commission's Science and Technology Action Plan on Innovation (23490712600); National Key Research and Development Program of China (2020YFA0803601); National Natural Science Foundation of China (National Science Foundation of China) (92068203, 91749103)
Citations: not cited yet (Europe PMC); 85 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above.

ChenYong-RU/MAXIM

License: GPL-3.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: df92e8d6cb999fea809dda3ee004079ea28cb20f, 25 February 2020
Languages: Python (4), Shell (1)
Size: 9 files, 5 scripts
Software Heritage: not archived
Found in: the text, “in situ CAPTURE 3C-seq”
Holds: README, license file, environment (setup.py)
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: pandas (3 files), Matplotlib (1 file), NumPy (1 file), pysam (1 file), SAMtools (1 file), SciPy (1 file), seaborn (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
7 files
At the source: github.com/ChenYong-RU/MAXIM

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 5 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1186/s13059-026-04098-8.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 24 authors, 7 keywords, 12 MeSH terms, 4 funders, 81 references.

Cite

This paper

Liu, J., Yin, Z., Peng, Y., Cui, S., Shi, B., Jiang, X., Yang, Z., Gu, S., Lin, Y., Xu, L., Xu, Z., Wang, X., Chen, T., Zhang, W., Wang, S., Xiao, Z., Huang, Z., Zhou, R., Yao, Z., . . . Guo, X. (2026). A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution. Genome biology, 27(1), 266. https://doi.org/10.1186/s13059-026-04098-8

BibTeX

@article{liu2026line,
author = {Liu, Jinhao and Yin, Zihang and Peng, Yonglin and Cui, Shuang and Shi, Bo and Jiang, Xinrui and Yang, Ziyi and Gu, Sijie and Lin, Yude and Xu, Lingfeng and Xu, Zhen and Wang, Xuankai and Chen, Tienan and Zhang, Wei and Wang, Shaojiao and Xiao, Zhiwei and Huang, Zhibo and Zhou, Rujiang and Yao, Zhengju and Zhao, Xiaodong and Guo, Ya and Xu, Shuhua and Li, Weidong and Guo, Xizhi},
title = {{A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution}},
journal = {Genome biology},
year = {2026},
month = may,
volume = {27},
number = {1},
pages = {266},
publisher = {BMC},
issn = {1474-7596},
doi = {10.1186/s13059-026-04098-8},
url = {https://doi.org/10.1186/s13059-026-04098-8},
pmid = {42071237},
pmcid = {PMC13501865}
}

RIS

TY - JOUR
AU - Liu, Jinhao
AU - Yin, Zihang
AU - Peng, Yonglin
AU - Cui, Shuang
AU - Shi, Bo
AU - Jiang, Xinrui
AU - Yang, Ziyi
AU - Gu, Sijie
AU - Lin, Yude
AU - Xu, Lingfeng
AU - Xu, Zhen
AU - Wang, Xuankai
AU - Chen, Tienan
AU - Zhang, Wei
AU - Wang, Shaojiao
AU - Xiao, Zhiwei
AU - Huang, Zhibo
AU - Zhou, Rujiang
AU - Yao, Zhengju
AU - Zhao, Xiaodong
AU - Guo, Ya
AU - Xu, Shuhua
AU - Li, Weidong
AU - Guo, Xizhi
TI - A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution
T2 - Genome biology
J2 - Genome Biol
PY - 2026
DA - 2026/05/04
VL - 27
IS - 1
SP - 266
SN - 1474-7596
PB - BMC
DO - 10.1186/s13059-026-04098-8
UR - https://doi.org/10.1186/s13059-026-04098-8
LA - en
ER -

CSL-JSON

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"title": "A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution",
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