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Add script to filter mashmap with tagged scaffolds #1

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Delphine-L
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From AGP files with Micro1 and Micro2 tags. Identify pairs and filter the mashmap output to keep only these pairs.
Could you try it out and see if it's helpful?
Run after the mashmap step and before the re-orientation

Delphine-L added 30 commits June 28, 2025 11:55
@Delphine-L
add script to filter mashmap with tagged scaffolds
4408407
@Delphine-L
generate file with pairs and orientation
cbab71e
@Delphine-L
simplify the script and generate the sak for reversing
bc9d0d6
@Delphine-L
improve help
569682b
@Delphine-L
remove hard paths and add argparser
ce13035
@Delphine-L
improve arguments and help
2817798
@Delphine-L
improve arguments and help
22a4e19
@Delphine-L
take file paths as inputs, and create directory if they don't exist
187d12e
@Delphine-L
replace stout by log file
afd3a45
@Delphine-L
fix help section
eeda5f1
@Delphine-L
now output hap2.vs.hap1.tsv file for ruby script
692c57a
@Delphine-L
update the run all script with the new args for the scripts
0a3b2cb
@Delphine-L
use the old pipeline without the micro tags
c2c4a69
@Delphine-L
Merge branch 'galaxy_ready' into filter_mashmap
763139a
@Delphine-L
replace ruby script with renaming the fasta files to use gfastats
3f221a2
@Delphine-L
fix bug with table separators
32e8644
@Delphine-L
fix renaming of agp columns that caused bug with unusual number of co…
5ecce9e 
…lumns
@Delphine-L
fix issues caused by irregular column number
457b2b6
@Delphine-L
Update dependencies and new usage
0120b05
@Delphine-L
remove obsolete scripts
f482fbb
@Delphine-L
remove the reading fasta message
0f8bcaf
@Delphine-L
now use hap1 and hap2 tags for pairing and takes the sex chromosome l…
8dc6a04 
…etter in input
@Delphine-L
improve logs, stop script if error, and add sex chromosome input
1ed4514
@Delphine-L
update README with correct tags and command lines
c9a11fd
@Delphine-L
correct help text, got the sex chrom for birds wring
4b26a0b
@Delphine-L
update instruction on tagging sex chromosomes
09b7f7e
@Delphine-L
add ouput and debugging
6eeef67
@Delphine-L
improve logs
f5da7b2
@Delphine-L
catch misssing arguments
c8cb724
@Delphine-L
add script to install dependencies
2ceff30
Delphine-L added 20 commits July 23, 2025 08:18
@Delphine-L
add script to install dependencies
a68d554
@Delphine-L
improve error reporting
c7677b2
@Delphine-L
fix issue with unloc renaming
a5bc0d6
@Delphine-L
Prepare for Packaging
a1f99de
@Delphine-L
Fix main functions
4ca8608
@Delphine-L
improve documentation
07c9c3b
@Delphine-L
improve documentation
d7375b9
@Delphine-L
Fix sex chromosome renaming
b3260b2
@Delphine-L
improve README
6b9d6c2
@Delphine-L
add channel for conda installs
cdd67f4
@Delphine-L
correct typo in script name
d370e42
@Delphine-L
Merge AGPcorrect, hap_split, and unloc
b0a37fd
@Delphine-L
update manuals
765c2d6
@Delphine-L
add error if pair missing in mashmap
c7536b6
@Delphine-L
fix renaming for pairs absent from mashmap
025dd65
@Delphine-L
put functions inside the script instead of in separate file
2f5c69c
@Delphine-L
fix typo
c5207f8
@Delphine-L
fix issue for heterogametic assemblies, add error for duplicated scaf…
e345a22 
…folds, remove sex chrom parameter
@Delphine-L
fix some missing unloc renaming
08c704f
@Delphine-L
skip renaming if not needed, and accelerate process with parrallel co…
bcd0733 
…mmands
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@Delphine-L