HOMGENEMAPPING(1)

🌸 HOMGENEMAPPING 💖

okay bestie so you found the HOMGENEMAPPING(1) page, and let me tell you, this is a good one. it's a little program called homGeneMapping and it's here to serve gene homology summaries ✨

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✨ NAME ✨

homGeneMapping — create summary of gene homology 🧬

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🎀 SYNOPSIS 🎀

homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.hal

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💅 DESCRIPTION 💅

so homGeneMapping takes a bunch of gene predictions from different genomes, plus a hal alignment of those genomes, and prints out a summary for each gene. it's giving ✨collab era✨. the summary tells you stuff like:

• how many of that gene's exons/introns are in agreement with genes of other genomes 🫶
• how many of its exons/introns are supported by extrinsic evidence from any of the genomes 🔬
• a list of geneids of homologous genes 👑

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👑 OPTIONS 👑

🌟 Mandatory parameters 🌟

these are not optional, bestie. no skipping. 💀

• --halfile=aln.hal — the input hal file 🧬
• --gtfs=gtffilenames.tbl — a text file holding the locations of the input gene files, and optionally the hints files, too (both of them are in GTF format). the file is formatted like this:

name_of_genome_1  path/to/genefile/of/genome_1  path/to/hintsfile/of/genome_1
name_of_genome_2  path/to/genefile/of/genome_2  path/to/hintsfile/of/genome_2
...
name_of_genome_N  path/to/genefile/of/genome_N  path/to/hintsfile/of/genome_N

🦋 Additional options 🦋

the extra toppings. sprinkle as needed. 🍓

• --cpus=N — N is the number of CPUs to use (default: 1) ⚡
• --noDupes — do not map between duplications in the hal graph (default: off) 🚫
• --details — print detailed output (default: off) 🔍
• --halLiftover_exec_dir=DIR — the directory that contains the executable halLiftover. if you don't specify it, then it has to be in the $PATH environment variable. iykyk 🙈
• --unmapped — print a GTF attribute with a list of all genomes that are not aligned to the corresponding gene feature, e.g. hgm_unmapped \"1,4,5\"; (default; off) 😭
• --tmpdir=DIR — a temporary file directory that stores lifted over files (default 'tmp/' in the current directory) 🗂️
• --outdir=DIR — file directory that stores output gene files (default: current directory) 📁
• --printHomologs=FILE — prints disjunct sets of homologous transcripts to FILE, e.g.

# 0     dana
# 1     dere
# 2     dgri
# 3     dmel
# 4     dmoj
# 5     dper
(0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
(1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
...

Two transcripts are in the same set if all their exons/introns are homologs and there are no additional exons/introns. 🧬 this option requires the Boost C++ Library 📚

• --dbaccess=db — retrieve hints from an SQLite database. in order to set up a database and populate it with hints, a separate tool 'load2sqlitedb' is provided. for more information, see the documentation in docs/RUNNING-AUGUSTUS-IN-CGP-MODE.md (DATABASE ACCESS / SQLite) in the Augustus package. if both a database and hint files in 'gtffilenames.tbl' are specified, hints are retrieved from both sources. double the hints, double the vibe 💖

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🌈 EXAMPLE 🌈

homGeneMapping --noDupes
--halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin
--gtfs=gtffilenames.tbl --halfile=msca.hal homGeneMapping
--gtfs=gtffilenames.tbl --halfile=aln.hal --outdir=outdir --cpus=4

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💜 AUTHORS 💜

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. legends fr fr 👑✨

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⭐ ADDITIONAL DOCUMENTATION ⭐

an exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. go read it, bestie, it's the whole lore 📖

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and that's the whole page, periodt. 💅 this was the HOMGENEMAPPING(1) manual page — that's the source vibe and the version tag of this lil doc — signing off with a 🎀 and a 🫶, go map some genes.