parseREDItools
parseREDItools takes RNA editing results called by
REDItools and saves them as a GVF
file. The GVF file can then be used to call variant peptides using
callVariant
Reference Version
The version of reference genome and proteome FASTA and annotation GTF MUST be consistent across all analysis.
Usage
usage: moPepGen parseREDItools [-h] -i <file> -o <file>
[--transcript-id-column <number>]
[--min-coverage-alt <number>]
[--min-frequency-alt <value>]
[--min-coverage-rna <value>]
[--min-coverage-dna <number>] --source SOURCE
[--skip-failed] [-a <file>]
[--reference-source {GENCODE,ENSEMBL}]
[--codon-table {Thraustochytrium Mitochondrial,SGC0,Gracilibacteria,Plant Plastid,SGC8,Chlorophycean Mitochondrial,Ascidian Mitochondrial,Invertebrate Mitochondrial,SGC5,SGC9,Blepharisma Macronuclear,Bacterial,SGC2,Yeast Mitochondrial,Pterobranchia Mitochondrial,Hexamita Nuclear,Echinoderm Mitochondrial,Euplotid Nuclear,Scenedesmus obliquus Mitochondrial,Pachysolen tannophilus Nuclear,Coelenterate Mitochondrial,Condylostoma Nuclear,SGC3,Protozoan Mitochondrial,SGC4,Peritrich Nuclear,Trematode Mitochondrial,Archaeal,Spiroplasma,Alternative Flatworm Mitochondrial,Mesodinium Nuclear,SGC1,Blastocrithidia Nuclear,Mold Mitochondrial,Alternative Yeast Nuclear,Standard,Flatworm Mitochondrial,Dasycladacean Nuclear,Vertebrate Mitochondrial,Karyorelict Nuclear,Balanophoraceae Plastid,Cephalodiscidae Mitochondrial,Candidate Division SR1,Ciliate Nuclear,Mycoplasma}]
[--chr-codon-table [CHR_CODON_TABLE ...]]
[--start-codons [START_CODONS ...]]
[--chr-start-codons [CHR_START_CODONS ...]]
[--index-dir [<file>]]
[--debug-level <value|number>] [-q]
Parse the REDItools result to a GVF format of variant records for moPepGen to
call variant peptides. The genome
options:
-h, --help show this help message and exit
-i <file>, --input-path <file>
File path to REDItools' TSV output. Valid formats:
['.tsv', '.txt'] (default: None)
-o <file>, --output-path <file>
File path to the output file. Valid formats: ['.gvf']
(default: None)
--transcript-id-column <number>
The column index for transcript ID. If your REDItools
table does not contains it, use the AnnotateTable.py
from the REDItools package. (default: 17)
--min-coverage-alt <number>
Minimal read coverage of alterations to be parsed.
(default: 3)
--min-frequency-alt <value>
Minimal frequency of alteration to be parsed.
(default: 0.1)
--min-coverage-rna <value>
Minimal read coverage at the alteration site of RNAseq
data of reference and all alterations. (default: 10)
--min-coverage-dna <number>
Minimal read coverage at the alteration site of WGS.
Set it to -1 to skip checking this. (default: 10)
--source SOURCE Variant source (e.g. gSNP, sSNV, Fusion) (default:
None)
--skip-failed When set, the failed records will be skipped.
(default: False)
--debug-level <value|number>
Debug level. (default: INFO)
-q, --quiet Quiet (default: False)
Reference Files:
-a <file>, --annotation-gtf <file>
Path to the annotation GTF file. Only ENSEMBL and
GENCODE are supported. Its version must be the same as
the genome and proteome FASTA. (default: None)
--reference-source {GENCODE,ENSEMBL}
Source of reference genome and annotation. (default:
None)
--codon-table {Thraustochytrium Mitochondrial,SGC0,Gracilibacteria,Plant Plastid,SGC8,Chlorophycean Mitochondrial,Ascidian Mitochondrial,Invertebrate Mitochondrial,SGC5,SGC9,Blepharisma Macronuclear,Bacterial,SGC2,Yeast Mitochondrial,Pterobranchia Mitochondrial,Hexamita Nuclear,Echinoderm Mitochondrial,Euplotid Nuclear,Scenedesmus obliquus Mitochondrial,Pachysolen tannophilus Nuclear,Coelenterate Mitochondrial,Condylostoma Nuclear,SGC3,Protozoan Mitochondrial,SGC4,Peritrich Nuclear,Trematode Mitochondrial,Archaeal,Spiroplasma,Alternative Flatworm Mitochondrial,Mesodinium Nuclear,SGC1,Blastocrithidia Nuclear,Mold Mitochondrial,Alternative Yeast Nuclear,Standard,Flatworm Mitochondrial,Dasycladacean Nuclear,Vertebrate Mitochondrial,Karyorelict Nuclear,Balanophoraceae Plastid,Cephalodiscidae Mitochondrial,Candidate Division SR1,Ciliate Nuclear,Mycoplasma}
Codon table. Defaults to "Standard". Supported codon
tables: {'Thraustochytrium Mitochondrial', 'SGC0',
'Gracilibacteria', 'Plant Plastid', 'SGC8',
'Chlorophycean Mitochondrial', 'Ascidian
Mitochondrial', 'Invertebrate Mitochondrial', 'SGC5',
'SGC9', 'Blepharisma Macronuclear', 'Bacterial',
'SGC2', 'Yeast Mitochondrial', 'Pterobranchia
Mitochondrial', 'Hexamita Nuclear', 'Echinoderm
Mitochondrial', 'Euplotid Nuclear', 'Scenedesmus
obliquus Mitochondrial', 'Pachysolen tannophilus
Nuclear', 'Coelenterate Mitochondrial', 'Condylostoma
Nuclear', 'SGC3', 'Protozoan Mitochondrial', 'SGC4',
'Peritrich Nuclear', 'Trematode Mitochondrial',
'Archaeal', 'Spiroplasma', 'Alternative Flatworm
Mitochondrial', 'Mesodinium Nuclear', 'SGC1',
'Blastocrithidia Nuclear', 'Mold Mitochondrial',
'Alternative Yeast Nuclear', 'Standard', 'Flatworm
Mitochondrial', 'Dasycladacean Nuclear', 'Vertebrate
Mitochondrial', 'Karyorelict Nuclear',
'Balanophoraceae Plastid', 'Cephalodiscidae
Mitochondrial', 'Candidate Division SR1', 'Ciliate
Nuclear', 'Mycoplasma'} (default: Standard)
--chr-codon-table [CHR_CODON_TABLE ...]
Chromosome specific codon table. Must be specified in
the format of "chrM:SGC1", where "chrM" is the
chromosome name and "SGC1" is the codon table to use
to translate genes on chrM. Supported codon tables:
{'Thraustochytrium Mitochondrial', 'SGC0',
'Gracilibacteria', 'Plant Plastid', 'SGC8',
'Chlorophycean Mitochondrial', 'Ascidian
Mitochondrial', 'Invertebrate Mitochondrial', 'SGC5',
'SGC9', 'Blepharisma Macronuclear', 'Bacterial',
'SGC2', 'Yeast Mitochondrial', 'Pterobranchia
Mitochondrial', 'Hexamita Nuclear', 'Echinoderm
Mitochondrial', 'Euplotid Nuclear', 'Scenedesmus
obliquus Mitochondrial', 'Pachysolen tannophilus
Nuclear', 'Coelenterate Mitochondrial', 'Condylostoma
Nuclear', 'SGC3', 'Protozoan Mitochondrial', 'SGC4',
'Peritrich Nuclear', 'Trematode Mitochondrial',
'Archaeal', 'Spiroplasma', 'Alternative Flatworm
Mitochondrial', 'Mesodinium Nuclear', 'SGC1',
'Blastocrithidia Nuclear', 'Mold Mitochondrial',
'Alternative Yeast Nuclear', 'Standard', 'Flatworm
Mitochondrial', 'Dasycladacean Nuclear', 'Vertebrate
Mitochondrial', 'Karyorelict Nuclear',
'Balanophoraceae Plastid', 'Cephalodiscidae
Mitochondrial', 'Candidate Division SR1', 'Ciliate
Nuclear', 'Mycoplasma'}. By default, "SGC1" is
assigned to mitochondrial chromosomes. (default: [])
--start-codons [START_CODONS ...]
Default start codon(s) to use for novel ORF
translation. Defaults to ["ATG"]. (default: ['ATG'])
--chr-start-codons [CHR_START_CODONS ...]
Chromosome specific start codon(s). For example,
"chrM:ATG,ATA,ATT".By defualt, mitochondrial
chromosome name is automatically inferred andstart
codon "ATG", "ATA", "ATT", "ATC" and "GTG" are
assigned to it. (default: [])
--index-dir [<file>] Path to the directory of index files generated by
moPepGen generateIndex. If given, --genome-fasta,
--proteome-fasta and --anntotation-gtf will be
ignored. (default: None)
Arguments
-h, --help
show this help message and exit
-i, --input-path <file> Path
File path to REDItools' TSV output. Valid formats: ['.tsv', '.txt']
-o, --output-path <file> Path
File path to the output file. Valid formats: ['.gvf']
--transcript-id-column <number> int
The column index for transcript ID. If your REDItools table does not contains it, use the AnnotateTable.py from the REDItools package.
int
Default: 17
--min-coverage-alt <number> int
Minimal read coverage of alterations to be parsed.
int
Default: 3
--min-frequency-alt <value> float
Minimal frequency of alteration to be parsed.
float
Default: 0.1
--min-coverage-rna <value> int
Minimal read coverage at the alteration site of RNAseq data of reference and all alterations.
int
Default: 10
--min-coverage-dna <number> int
Minimal read coverage at the alteration site of WGS. Set it to -1 to skip checking this.
int
Default: 10
--source str
Variant source (e.g. gSNP, sSNV, Fusion)
--skip-failed
When set, the failed records will be skipped.
Default: False
-a, --annotation-gtf <file> Path
Path to the annotation GTF file. Only ENSEMBL and GENCODE are supported. Its version must be the same as the genome and proteome FASTA.
--reference-source str
Source of reference genome and annotation.
Choices: ['GENCODE', 'ENSEMBL']
--codon-table str
Codon table. Defaults to "Standard". Supported codon tables: {'Thraustochytrium Mitochondrial', 'SGC0', 'Gracilibacteria', 'Plant Plastid', 'SGC8', 'Chlorophycean Mitochondrial', 'Ascidian Mitochondrial', 'Invertebrate Mitochondrial', 'SGC5', 'SGC9', 'Blepharisma Macronuclear', 'Bacterial', 'SGC2', 'Yeast Mitochondrial', 'Pterobranchia Mitochondrial', 'Hexamita Nuclear', 'Echinoderm Mitochondrial', 'Euplotid Nuclear', 'Scenedesmus obliquus Mitochondrial', 'Pachysolen tannophilus Nuclear', 'Coelenterate Mitochondrial', 'Condylostoma Nuclear', 'SGC3', 'Protozoan Mitochondrial', 'SGC4', 'Peritrich Nuclear', 'Trematode Mitochondrial', 'Archaeal', 'Spiroplasma', 'Alternative Flatworm Mitochondrial', 'Mesodinium Nuclear', 'SGC1', 'Blastocrithidia Nuclear', 'Mold Mitochondrial', 'Alternative Yeast Nuclear', 'Standard', 'Flatworm Mitochondrial', 'Dasycladacean Nuclear', 'Vertebrate Mitochondrial', 'Karyorelict Nuclear', 'Balanophoraceae Plastid', 'Cephalodiscidae Mitochondrial', 'Candidate Division SR1', 'Ciliate Nuclear', 'Mycoplasma'}
str
Default: Standard
Choices: {'Thraustochytrium Mitochondrial', 'SGC0', 'Gracilibacteria', 'Plant Plastid', 'SGC8', 'Chlorophycean Mitochondrial', 'Ascidian Mitochondrial', 'Invertebrate Mitochondrial', 'SGC5', 'SGC9', 'Blepharisma Macronuclear', 'Bacterial', 'SGC2', 'Yeast Mitochondrial', 'Pterobranchia Mitochondrial', 'Hexamita Nuclear', 'Echinoderm Mitochondrial', 'Euplotid Nuclear', 'Scenedesmus obliquus Mitochondrial', 'Pachysolen tannophilus Nuclear', 'Coelenterate Mitochondrial', 'Condylostoma Nuclear', 'SGC3', 'Protozoan Mitochondrial', 'SGC4', 'Peritrich Nuclear', 'Trematode Mitochondrial', 'Archaeal', 'Spiroplasma', 'Alternative Flatworm Mitochondrial', 'Mesodinium Nuclear', 'SGC1', 'Blastocrithidia Nuclear', 'Mold Mitochondrial', 'Alternative Yeast Nuclear', 'Standard', 'Flatworm Mitochondrial', 'Dasycladacean Nuclear', 'Vertebrate Mitochondrial', 'Karyorelict Nuclear', 'Balanophoraceae Plastid', 'Cephalodiscidae Mitochondrial', 'Candidate Division SR1', 'Ciliate Nuclear', 'Mycoplasma'}
--chr-codon-table str
Chromosome specific codon table. Must be specified in the format of "chrM:SGC1", where "chrM" is the chromosome name and "SGC1" is the codon table to use to translate genes on chrM. Supported codon tables: {'Thraustochytrium Mitochondrial', 'SGC0', 'Gracilibacteria', 'Plant Plastid', 'SGC8', 'Chlorophycean Mitochondrial', 'Ascidian Mitochondrial', 'Invertebrate Mitochondrial', 'SGC5', 'SGC9', 'Blepharisma Macronuclear', 'Bacterial', 'SGC2', 'Yeast Mitochondrial', 'Pterobranchia Mitochondrial', 'Hexamita Nuclear', 'Echinoderm Mitochondrial', 'Euplotid Nuclear', 'Scenedesmus obliquus Mitochondrial', 'Pachysolen tannophilus Nuclear', 'Coelenterate Mitochondrial', 'Condylostoma Nuclear', 'SGC3', 'Protozoan Mitochondrial', 'SGC4', 'Peritrich Nuclear', 'Trematode Mitochondrial', 'Archaeal', 'Spiroplasma', 'Alternative Flatworm Mitochondrial', 'Mesodinium Nuclear', 'SGC1', 'Blastocrithidia Nuclear', 'Mold Mitochondrial', 'Alternative Yeast Nuclear', 'Standard', 'Flatworm Mitochondrial', 'Dasycladacean Nuclear', 'Vertebrate Mitochondrial', 'Karyorelict Nuclear', 'Balanophoraceae Plastid', 'Cephalodiscidae Mitochondrial', 'Candidate Division SR1', 'Ciliate Nuclear', 'Mycoplasma'}. By default, "SGC1" is assigned to mitochondrial chromosomes.
str
Default: []
--start-codons str
Default start codon(s) to use for novel ORF translation. Defaults to ["ATG"].
str
Default: ['ATG']
--chr-start-codons str
Chromosome specific start codon(s). For example, "chrM:ATG,ATA,ATT".By defualt, mitochondrial chromosome name is automatically inferred andstart codon "ATG", "ATA", "ATT", "ATC" and "GTG" are assigned to it.
str
Default: []
--index-dir <file> Path
Path to the directory of index files generated by moPepGen generateIndex. If given, --genome-fasta, --proteome-fasta and --anntotation-gtf will be ignored.
--debug-level <value|number> str
Debug level.
str
Default: INFO
-q, --quiet
Quiet
Default: False