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FastOMA Subpackages
Sina Majidian edited this page Feb 4, 2025
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FastOMA benefits from four sub-packages, written in Python.
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fastoma-check-input
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fastoma-infer-roothogs
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fastoma-batch-roothogs
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fastoma-infer-subhogs
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fastoma-collect-subhogs
You can edit the fastoma Nextflow pipeline at FastOMA.nf using different arguments or threshold tailored for your analysis.
$ fastoma-check-input -h
usage: fastoma-check-input [-h] [--version] --proteomes PROTEOMES --species-tree SPECIES_TREE --out-tree
OUT_TREE [--splice SPLICE] [--hogmap HOGMAP] [--omamer_db OMAMER_DB] [-v]
checking parameters for FastOMA
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--proteomes PROTEOMES
Path to the folder containing the input proteomes
--species-tree SPECIES_TREE
Path to the input species tree file in newick format
--out-tree OUT_TREE Path to output file for sanitised species tree.
--splice SPLICE Path to the folder containing the splice information files
--hogmap HOGMAP Path to the folder containing the hogmap files
--omamer_db OMAMER_DB
Path to the omamer database
-v Increase verbosity to info/debug
$ fastoma-infer-roothogs -h
usage: fastoma-infer-roothogs [-h] [--version] --proteomes PROTEOMES [--splice SPLICE] [--hogmap HOGMAP]
--out-rhog-folder OUT_RHOG_FOLDER [-v]
[--min-sequence-length MIN_SEQUENCE_LENGTH]
[--mergHOG-ratioMax-thresh MERGHOG_RATIOMAX_THRESH]
[--mergHOG-ratioMin-thresh MERGHOG_RATIOMIN_THRESH]
[--mergHOG-shared-thresh MERGHOG_SHARED_THRESH]
[--mergHOG-fscore-thresh MERGHOG_FSCORE_THRESH]
[--big-rhog-size BIG_RHOG_SIZE] [--big-fscore-thresh BIG_FSCORE_THRESH]
checking parameters for FastOMA
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--proteomes PROTEOMES
Path to the folder containing the input proteomes
--splice SPLICE Path to the folder containing the splice information files
--hogmap HOGMAP Path to the folder containing the hogmap files
--out-rhog-folder OUT_RHOG_FOLDER
Folder where the roothog fasta files are written
-v Increase verbosity to info/debug
--min-sequence-length MIN_SEQUENCE_LENGTH
minimum sequence length. Shorter sequences will be ignored. (Default=50)
--mergHOG-ratioMax-thresh MERGHOG_RATIOMAX_THRESH
For merging rootHOGs, threshold of ratioMax
--mergHOG-ratioMin-thresh MERGHOG_RATIOMIN_THRESH
For merging rootHOGs, threshold of ratioMin
--mergHOG-shared-thresh MERGHOG_SHARED_THRESH
For merging rootHOGs, threshold of number shared proteins
--mergHOG-fscore-thresh MERGHOG_FSCORE_THRESH
For merging rootHOGs, threshold of famlut score shared proteins
--big-rhog-size BIG_RHOG_SIZE
For big rootHOGs, we have different heuristics
--big-fscore-thresh BIG_FSCORE_THRESH
For huge rootHOGs, we have different heuristics, like filtering low family score
protiens
$ fastoma-batch-roothogs -h
usage: fastoma-batch-roothogs [-h] [--version] --input-roothogs INPUT_ROOTHOGS --out-big OUT_BIG
--out-rest OUT_REST [-v]
Analyse roothog families and create batches for analysis
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--input-roothogs INPUT_ROOTHOGS
folder where input roothogs are stored
--out-big OUT_BIG folder where the big single family hogs should be stored
--out-rest OUT_REST folder where the remaining families should be stored inbatch subfolder
structure.
-v incrase verbosity
$ fastoma-infer-subhogs -h
usage: fastoma-infer-subhogs [-h] [--version] --input-rhog-folder INPUT_RHOG_FOLDER [--parallel]
--species-tree SPECIES_TREE [--output-pickles OUTPUT_PICKLES]
[--threshold-dubious-sd THRESHOLD_DUBIOUS_SD]
[--number-of-samples-per-hog NUMBER_OF_SAMPLES_PER_HOG]
[--overlap-fragments OVERLAP_FRAGMENTS]
[--gene-rooting-method GENE_ROOTING_METHOD] [--gene-trees-write]
[--msa-write]
[--msa-filter-method {col-row-threshold,col-elbow-row-threshold,trimal}]
[--gap-ratio-row GAP_RATIO_ROW] [--gap-ratio-col GAP_RATIO_COL]
[--min-col-trim MIN_COL_TRIM] [-v]
checking parameters for FastOMA
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--input-rhog-folder INPUT_RHOG_FOLDER
Path to the input rootHOG folder. (default: None)
--parallel use concurrent parallel per rootHOG (default: False)
--species-tree SPECIES_TREE
Path to the input species tree file in newick format (default: None)
--output-pickles OUTPUT_PICKLES
Path to the output folder (default: pickle_hogs)
--threshold-dubious-sd THRESHOLD_DUBIOUS_SD
Threshold to remove proteins in a gene tree due to low species overlap score,
not enough evidence for duplication event. (default: 0.1)
--number-of-samples-per-hog NUMBER_OF_SAMPLES_PER_HOG
Number of representatives (sequences) per HOG. Defaults to (default: 20)
--overlap-fragments OVERLAP_FRAGMENTS
Threshold overlap between two sequences (rows) in MSA to decide whether they are
fragments of a gene. (default: 0.15)
--gene-rooting-method GENE_ROOTING_METHOD
The method used for rooting of gene tree : midpoint mad Nevers_rooting .
(default: midpoint)
--gene-trees-write writing the all gene trees . (default: False)
--msa-write writing the raw MSAs (might have more genes that the final gene tree). (default:
False)
--msa-filter-method {col-row-threshold,col-elbow-row-threshold,trimal}
The method used for filtering MSAs. (default: col-row-threshold)
--gap-ratio-row GAP_RATIO_ROW
For trimming the MSA, the threshold of ratio of gaps for each row. (default:
0.3)
--gap-ratio-col GAP_RATIO_COL
For trimming the MSA, the threshold of ratio of gaps for each column. (default:
0.5)
--min-col-trim MIN_COL_TRIM
min no. columns in msa to consider for filtering (default: 50)
-v Increase verbosity to info/debug (default: 0)
$ fastoma-collect-subhogs -h
usage: fastoma-collect-subhogs [-h] [--version] --pickle-folder PICKLE_FOLDER --roothogs-folder
ROOTHOGS_FOLDER --gene-id-pickle-file GENE_ID_PICKLE_FILE [--out OUT]
[-v] [--roothog-tsv ROOTHOG_TSV]
[--marker-groups-fasta MARKER_GROUPS_FASTA] --species-tree SPECIES_TREE
[--id-transform {UniProt,noop}]
collecting all computed HOGs and combine into a single orthoxml
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--pickle-folder PICKLE_FOLDER
folder containing the pickle files. Will be searched recursively
--roothogs-folder ROOTHOGS_FOLDER
folder containing the omamer roothogs
--gene-id-pickle-file GENE_ID_PICKLE_FILE
file containing the gene-id dictionary in pickle format
--out OUT output filename in orthoxml
-v
--roothog-tsv ROOTHOG_TSV
If specified, a tsv file with the given path will be produced containing the
roothog assignments as TSV file. In addition, a folder named RootHOGsFasta will
be generatedwith one fasta file per inferred RootHOG.
--marker-groups-fasta MARKER_GROUPS_FASTA
If specified, a folder named OrthologousFasta and a TSV file with the name
provided in this argument will be generated that contains single copy groups,
i.e. groups which have at most one gene per species. Useful as phylogenetic
marker genes to reconstruct species trees.
--species-tree SPECIES_TREE
Path to the species tree used to infer the hogs
--id-transform {UniProt,noop}
ID transformer from fasta files to orthoxml / OrthologGroup protein IDs. By
default, no transformation will be done. Existing values are: noop: No
transformation - entire ID of fasta header UniProt: '>sp|P68250|1433B_BOVIN' -->
P68250
If you want to use QFO benchmark or the online version https://orthology.benchmarkservice.org/proxy/, you need to activate --id-transform UniProt.
fastoma-helper -h
usage: fastoma-helper [-h] [-v] {pw-rel} ...
FastOMA helper scripts
positional arguments:
{pw-rel}
optional arguments:
-h, --help show this help message and exit
-v increase verbosity