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chromsyn's Introduction

SLiMSuite

Open source short linear motif discovery and sequence analysis.

This repository contains the core code for the SLiMSuite package of short linear motif (SLiM) discovery and sequence analysis tools from the Edwards Lab.

A summary of SLiMSuite and SeqSuite tools can be found in PROGRAMS.md. More information can be found at the SLiMSuite Blog and in the docs/ folder. Release information can be found in RELEASE.txt. Please see release_notes.txt and individual modules for a summary of update history. Additional documentation can be found at the SLiMSuite GitHub Pages site.

If you have any questions, raise an issue or contact the author.

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wook2014 yuzhenpeng solaymane tzhang-nmdp

chromsyn's Issues

Excecution Halted 

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Registered S3 method overwritten by 'rvest':
  method            from
  read_xml.response xml2
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
[Fri Aug  4 08:16:43 2023] ../rje_load.R
[Fri Aug  4 08:16:43 2023] Sequence FOFN File: sequences.fofn
[Fri Aug  4 08:16:43 2023] No region data file given.
[Fri Aug  4 08:16:43 2023] TIDK FOFN file: tidk.fofn
[Fri Aug  4 08:16:43 2023] Assembly gap FOFN file: gaps.fofn
[Fri Aug  4 08:16:43 2023] features table FOFN file not found: ft.fofn
[Fri Aug  4 08:16:43 2023] BUSCO full FOFN file: busco.fofn
[Fri Aug  4 08:16:43 2023] BUSCO FOFN file: busco.fofn
[Fri Aug  4 08:16:43 2023] #RCODE Setup complete.
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames loaded from sequences.fofn
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames loaded from busco.fofn
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames after filtering to recognised genomes.
[Fri Aug  4 08:16:43 2023] Genomes (order=LIST): ensPLATY, ensPOTO1, ensTAMM
Joining, by = "Genome"
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames loaded from tidk.fofn
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames after filtering to recognised genomes.
Joining, by = "Genome"
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames loaded from gaps.fofn
[Fri Aug  4 08:16:43 2023] #FOFN 3 filenames after filtering to recognised genomes.
Joining, by = "Genome"
[Fri Aug  4 08:16:43 2023] #GENOME  3 genomes: ensPLATY, ensPOTO1, ensTAMM
[Fri Aug  4 08:16:43 2023] ensPLATY...
Error in all_of(keepfields) : could not find function "all_of"
Calls: seqTable ... <Anonymous> -> vars_select_eval -> map_if -> map -> .f
Execution halted


Error in all_of(keepfields) : could not find function "all_of"
Calls: seqTable ... <Anonymous> -> vars_select_eval -> map_if -> map -> .f
Execution halted

I was able to create all of the files but then it failed. Am I missing some package? Any help would be greatly appreciated!

Busco v5 format is recognized as v3

Hello, thanks for making this tool! I'm trying to run chromsyn but I get this error:

Rscript chromsyn.R busco=busco.fofn seqeuneces=sequences.fofn focus=scaffold16_size3654323

[Sun Jul 16 11:20:19 2023] #FOFN 12 filenames loaded from sequences.fofn
[Sun Jul 16 11:20:19 2023] #FOFN 12 filenames loaded from busco.fofn
[Sun Jul 16 11:20:19 2023] #FOFN 12 filenames after filtering to recognised genomes.
[Sun Jul 16 11:20:19 2023] Genomes (order=LIST): scaffold13_size4067469, scaffold14_size3830318, scaffold15_size3669401, scaffold16_size3654323, scaffold23_size2881292, scaffold27_size2720374, scaffold28_size2676831, scaffold2_size7801212, scaffold3_size7411349, scaffold5_size6470894, scaffold6_size5997242, scaffold7_size5813896
Joining with `by = join_by(Genome)`
[Sun Jul 16 11:20:19 2023] #GENOME  12 genomes: scaffold13_size4067469, scaffold14_size3830318, scaffold15_size3669401, scaffold16_size3654323, scaffold23_size2881292, scaffold27_size2720374, scaffold28_size2676831, scaffold2_size7801212, scaffold3_size7411349, scaffold5_size6470894, scaffold6_size5997242, scaffold7_size5813896
[Sun Jul 16 11:20:19 2023] scaffold13_size4067469...
[Sun Jul 16 11:20:19 2023] #SEQS 1 scaffold13_size4067469 sequences loaded from gendata/scaffold13_size4067469.telomeres.tdt
[Sun Jul 16 11:20:19 2023] #SEQS 1 scaffold13_size4067469 sequences meet minlen cutoff of 0 bp
[Sun Jul 16 11:20:19 2023] #BUSCOV BUSCO v3 format
Error in names(x) <- value : 
  'names' attribute [7] must be the same length as the vector [2]
Calls: buscoTable -> colnames<-
Execution halted

It seems to think the format is v3, but this is what my scaffold13_size4067469.busco5.tsv looks like:

# BUSCO version is: 5.4.2 
# The lineage dataset is: chlorophyta_odb10 (Creation date: 2020-08-05, number of genomes: 16, number of BUSCOs: 1519)
# Busco id      Status  Sequence        Gene Start      Gene End        Strand  Score   Length  OrthoDB url     Description
15at3041        Missing
42at3041        Missing
45at3041        Missing
52at3041        Missing
etc...

Any ideas on how to fix this?

Conflicts tidyverse

Hi

I got conflict problems due to the tidy verse package.
something like:

Conflicts --------------------------------------------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
i Use the conflicted package to force all conflicts to become errors
[Fri Dec 1 15:36:58 2023] chromsyn/rje_load.R
[Fri Dec 1 15:36:58 2023] Sequence FOFN File: sequences.fofn
[Fri Dec 1 15:36:58 2023] Cannot find sequence FOFN file: sequences.fofn

Here is the solution:

  1. install package conflicted (e.g. install.packages("conflicted", lib="/usr/lib/R/library"))

Than add to line 122 of chromosyn.R:

library(conflicted)
library(tidyverse)
conflict_prefer("filter", "dplyr")
conflict_prefer("lag", "dplyr")

And it will work

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