Read files in various standard formats (FASTA, GFF3, GBK, BED, BLAST, ...) into track tables
Source:R/read.R, R/read_feats.R, R/read_seqs.R
read_tracks.RdConvenience functions to read sequences, features or links from various
bioinformatics file formats, such as FASTA, GFF3, Genbank, BLAST tabular
output, etc. See def_formats() for full list. File formats and the
corresponding read-functions are automatically determined based on file
extensions. All these functions can read multiple files in the same format at
once, and combine them into a single table - useful, for example, to read a
folder of gff-files with each file containing genes of a different genome.
Usage
read_feats(files, .id = "file_id", format = NULL, parser = NULL, ...)
read_subfeats(files, .id = "file_id", format = NULL, parser = NULL, ...)
read_links(files, .id = "file_id", format = NULL, parser = NULL, ...)
read_sublinks(files, .id = "file_id", format = NULL, parser = NULL, ...)
read_seqs(
files,
.id = "file_id",
format = NULL,
parser = NULL,
parse_desc = TRUE,
...
)Arguments
- files
files to reads. Should all be of same format. In many cases, compressed files (
.gz,.bz2,.xz, or.zip) are supported. Similarly, automatic download of remote files starting withhttp(s)://orftp(s)://works in most cases.- .id
the column with the name of the file a record was read from. Defaults to "file_id". Set to "bin_id" if every file represents a different bin.
- format
specify a format known to gggenomes, such as
gff3,gbk, ... to overwrite automatic determination based on the file extension (seedef_formats()for full list).- parser
specify the name of an R function to overwrite automatic determination based on format, e.g.
parser="read_tsv".- ...
additional arguments passed on to the format-specific read function called down the line.
- parse_desc
turn
key=some valuepairs fromseq_descintokey-named columns and remove them fromseq_desc.
Value
A gggenomes-compatible sequence, feature or link tibble
tibble with features
tibble with features
tibble with links
tibble with links
tibble with sequence information
Functions
read_feats(): read files as features mapping onto sequences.read_subfeats(): read files as subfeatures mapping onto other featuresread_links(): read files as links connecting sequencesread_sublinks(): read files as sublinks connecting featuresread_seqs(): read sequence ID, description and length.
Examples
# read genes/features from a gff file
read_feats(ex("eden-utr.gff"))
#> Reading 'gff3' with `read_gff3()`:
#> * file_id: eden-utr [/home/runner/work/_temp/Library/gggenomes/extdata/eden-utr.gff]
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> • Parent -> parent_ids
#> • Target -> target
#> Features read
#> # A tibble: 8 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 NA CDS 5
#> 2 NA TF_binding_site 1
#> 3 NA cDNA_match 1
#> 4 NA exon 5
#> 5 NA five_prime_UTR 1
#> 6 NA gene 1
#> 7 NA mRNA 5
#> 8 NA three_prime_UTR 1
#> # A tibble: 20 × 15
#> file_id seq_id start end strand type feat_id introns parent_ids source
#> <chr> <chr> <int> <int> <chr> <chr> <chr> <list> <list> <chr>
#> 1 eden-utr ctg123 1000 9000 + gene gene00… <NULL> <chr [1]> NA
#> 2 eden-utr ctg123 1000 1012 + TF_bind… tfbs00… <NULL> <chr [1]> NA
#> 3 eden-utr ctg123 1050 9000 + mRNA mRNA00… <dbl> <chr [1]> NA
#> 4 eden-utr ctg123 1050 9000 + mRNA mRNA00… <dbl> <chr [1]> NA
#> 5 eden-utr ctg123 1300 9000 + mRNA mRNA00… <dbl> <chr [1]> NA
#> 6 eden-utr ctg123 1300 9000 + mRNA mRNA00… <dbl> <chr [1]> NA
#> 7 eden-utr ctg123 1300 1500 + exon exon00… <NULL> <chr [1]> NA
#> 8 eden-utr ctg123 1050 1500 + exon exon00… <NULL> <chr [2]> NA
#> 9 eden-utr ctg123 3000 3902 + exon exon00… <NULL> <chr [2]> NA
#> 10 eden-utr ctg123 5000 5500 + exon exon00… <NULL> <chr [3]> NA
#> 11 eden-utr ctg123 7000 9000 + exon exon00… <NULL> <chr [3]> NA
#> 12 eden-utr ctg123 1201 7600 + CDS cds000… <dbl> <chr [1]> NA
#> 13 eden-utr ctg123 1201 7600 + CDS cds000… <dbl> <chr [1]> NA
#> 14 eden-utr ctg123 3301 7600 + CDS cds000… <dbl> <chr [1]> NA
#> 15 eden-utr ctg123 3391 7600 + CDS cds000… <dbl> <chr [1]> NA
#> 16 eden-utr ctg123 1050 9000 + mRNA mRNA00… <int> <chr [1]> NA
#> 17 eden-utr ctg123 1050 1200 + five_pr… feat_25 <NULL> <chr [1]> NA
#> 18 eden-utr ctg123 1201 7600 + CDS cds000… <dbl> <chr [1]> NA
#> 19 eden-utr ctg123 7601 9000 + three_p… feat_30 <NULL> <chr [1]> NA
#> 20 eden-utr ctg123 1050 9000 + cDNA_ma… match0… <dbl> <chr [1]> NA
#> # ℹ 5 more variables: score <chr>, phase <chr>, name <chr>, target <chr>,
#> # geom_id <chr>
# read all gff files from a directory
read_feats(list.files(ex("emales/"), "*.gff$", full.names = TRUE))
#> Reading 'gff3' with `read_gff3()`:
#> * file_id: emales-ngaros [/home/runner/work/_temp/Library/gggenomes/extdata/emales//emales-ngaros.gff]
#> Harmonizing attribute names
#> • ID -> feat_id
#> Features read
#> # A tibble: 1 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 MFG repeat_region 3
#> * file_id: emales-tirs [/home/runner/work/_temp/Library/gggenomes/extdata/emales//emales-tirs.gff]
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> Features read
#> # A tibble: 1 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 MFG repeat_region 12
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales//emales.gff]
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> • Note -> note
#> Features read
#> # A tibble: 1 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 MFG CDS 143
#> # A tibble: 158 × 17
#> file_id seq_id start end strand type feat_id introns parent_ids source
#> <chr> <chr> <int> <int> <chr> <chr> <chr> <list> <list> <chr>
#> 1 emales-nga… BVI_0… 11043 17065 NA repe… nBVI_0… <NULL> <chr [1]> MFG
#> 2 emales-nga… BVI_0… 7894 14280 NA repe… nBVI_0… <NULL> <chr [1]> MFG
#> 3 emales-nga… E4-10… 2854 9283 NA repe… nE4-10… <NULL> <chr [1]> MFG
#> 4 emales-tirs BVI_0… 1 473 + repe… BVI_00… <NULL> <chr [1]> MFG
#> 5 emales-tirs BVI_0… 26348 26820 - repe… BVI_00… <NULL> <chr [1]> MFG
#> 6 emales-tirs BVI_0… 1 488 + repe… BVI_06… <NULL> <chr [1]> MFG
#> 7 emales-tirs BVI_0… 26321 26808 - repe… BVI_06… <NULL> <chr [1]> MFG
#> 8 emales-tirs Cflag… 1 1081 + repe… Cflag_… <NULL> <chr [1]> MFG
#> 9 emales-tirs Cflag… 20231 21311 - repe… Cflag_… <NULL> <chr [1]> MFG
#> 10 emales-tirs E4-10… 1 319 + repe… E4-10_… <NULL> <chr [1]> MFG
#> # ℹ 148 more rows
#> # ℹ 7 more variables: score <chr>, phase <chr>, name <chr>, geom_id <chr>,
#> # width <chr>, gc_content <chr>, note <chr>
# read remote files
# \donttest{
gbk_phages <- c(
PSSP7 = paste0(
"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/",
"000/858/745/GCF_000858745.1_ViralProj15134/",
"GCF_000858745.1_ViralProj15134_genomic.gff.gz"
),
PSSP3 = paste0(
"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/",
"000/904/555/GCF_000904555.1_ViralProj195517/",
"GCF_000904555.1_ViralProj195517_genomic.gff.gz"
)
)
read_feats(gbk_phages)
#> Reading 'gff3' with `read_gff3()`:
#> * file_id: PSSP7 [ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/858/745/GCF_000858745.1_ViralProj15134/GCF_000858745.1_ViralProj15134_genomic.gff.gz]
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Dbxref -> dbxref
#> • old-name -> old_name
#> • Name -> name
#> • Parent -> parent_ids
#> • Note -> note
#> Features read
#> # A tibble: 4 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 RefSeq CDS 58
#> 2 RefSeq gene 58
#> 3 RefSeq region 1
#> 4 RefSeq sequence_feature 1
#> * file_id: PSSP3 [ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/904/555/GCF_000904555.1_ViralProj195517/GCF_000904555.1_ViralProj195517_genomic.gff.gz]
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Dbxref -> dbxref
#> • collection-date -> collection_date
#> • isolation-source -> isolation_source
#> • lab-host -> lab_host
#> • lat-lon -> lat_lon
#> • Name -> name
#> • Parent -> parent_ids
#> • Note -> note
#> Features read
#> # A tibble: 4 × 3
#> source type n
#> <chr> <chr> <int>
#> 1 RefSeq CDS 53
#> 2 RefSeq gene 53
#> 3 RefSeq pseudogene 3
#> 4 RefSeq region 1
#> # A tibble: 228 × 36
#> file_id seq_id start end strand type feat_id introns parent_ids source
#> <chr> <chr> <int> <int> <chr> <chr> <chr> <list> <list> <chr>
#> 1 PSSP7 NC_006882… 1 45176 + regi… NC_006… <NULL> <chr [1]> RefSeq
#> 2 PSSP7 NC_006882… 1079 1816 + gene gene-P… <int> <chr [1]> RefSeq
#> 3 PSSP7 NC_006882… 1079 1816 + CDS cds-YP… <NULL> <chr [1]> RefSeq
#> 4 PSSP7 NC_006882… 1845 2423 + gene gene-P… <int> <chr [1]> RefSeq
#> 5 PSSP7 NC_006882… 1845 2423 + CDS cds-YP… <NULL> <chr [1]> RefSeq
#> 6 PSSP7 NC_006882… 2637 2903 + gene gene-P… <int> <chr [1]> RefSeq
#> 7 PSSP7 NC_006882… 2637 2903 + CDS cds-YP… <NULL> <chr [1]> RefSeq
#> 8 PSSP7 NC_006882… 2900 3130 + gene gene-P… <int> <chr [1]> RefSeq
#> 9 PSSP7 NC_006882… 2900 3130 + CDS cds-YP… <NULL> <chr [1]> RefSeq
#> 10 PSSP7 NC_006882… 3127 3291 + gene gene-P… <int> <chr [1]> RefSeq
#> # ℹ 218 more rows
#> # ℹ 26 more variables: score <chr>, phase <chr>, name <chr>, dbxref <chr>,
#> # gbkey <chr>, genome <chr>, mol_type <chr>, old_name <chr>,
#> # gene_biotype <chr>, locus_tag <chr>, experiment <chr>, product <chr>,
#> # protein_id <chr>, transl_table <chr>, gene <chr>, note <chr>,
#> # geom_id <chr>, collection_date <chr>, isolation_source <chr>,
#> # lab_host <chr>, lat_lon <chr>, strain <chr>, description <chr>, …
# }
# read sequences from a fasta file.
read_seqs(ex("emales/emales.fna"), parse_desc = FALSE)
#> Reading 'fasta' with `read_seq_len()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.fna]
#> # A tibble: 6 × 4
#> file_id seq_id seq_desc length
#> <chr> <chr> <chr> <int>
#> 1 emales BVI_008A emale_type=EMALE01 is_typespecies=FALSE has_tir=TR… 26820
#> 2 emales BVI_069 emale_type=EMALE01 is_typespecies=FALSE has_tir=TR… 26808
#> 3 emales Cflag_017B emale_type=EMALE01 is_typespecies=TRUE has_tir=TRUE 21311
#> 4 emales E4-10_086 emale_type=EMALE01 is_typespecies=FALSE has_tir=TR… 20642
#> 5 emales E4-10_112 emale_type=EMALE01 is_typespecies=FALSE has_tir=TR… 26856
#> 6 emales RCC970_016B emale_type=EMALE01 is_typespecies=FALSE has_tir=TR… 20152
# read sequence info from a fasta file with `parse_desc=TRUE` (default). `key=value`
# pairs are removed from `seq_desc` and parsed into columns with `key` as name
read_seqs(ex("emales/emales.fna"))
#> Reading 'fasta' with `read_seq_len()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.fna]
#> # A tibble: 6 × 7
#> file_id seq_id seq_desc length emale_type is_typespecies has_tir
#> <chr> <chr> <chr> <int> <chr> <lgl> <lgl>
#> 1 emales BVI_008A NA 26820 EMALE01 FALSE TRUE
#> 2 emales BVI_069 NA 26808 EMALE01 FALSE TRUE
#> 3 emales Cflag_017B NA 21311 EMALE01 TRUE TRUE
#> 4 emales E4-10_086 NA 20642 EMALE01 FALSE TRUE
#> 5 emales E4-10_112 NA 26856 EMALE01 FALSE TRUE
#> 6 emales RCC970_016B NA 20152 EMALE01 FALSE TRUE
# read sequence info from samtools/seqkit style index
read_seqs(ex("emales/emales.fna.seqkit.fai"))
#> Reading 'fai' with `read_fai()`:
#> * file_id: emales.fna.seqkit [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.fna.seqkit.fai]
#> # A tibble: 6 × 7
#> file_id seq_id seq_desc length emale_type is_typespecies has_tir
#> <chr> <chr> <chr> <int> <chr> <lgl> <lgl>
#> 1 emales.fna.seqkit BVI_008A NA 26820 EMALE01 FALSE TRUE
#> 2 emales.fna.seqkit BVI_069 NA 26808 EMALE01 FALSE TRUE
#> 3 emales.fna.seqkit Cflag_017B NA 21311 EMALE01 TRUE TRUE
#> 4 emales.fna.seqkit E4-10_086 NA 20642 EMALE01 FALSE TRUE
#> 5 emales.fna.seqkit E4-10_112 NA 26856 EMALE01 FALSE TRUE
#> 6 emales.fna.seqkit RCC970_01… NA 20152 EMALE01 FALSE TRUE
# read sequence info from multiple gff file
read_seqs(c(ex("emales/emales.gff"), ex("emales/emales-tirs.gff")))
#> Reading 'gff3' with `read_seq_len()`:
#> * file_id: emales [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales.gff]
#> * file_id: emales-tirs [/home/runner/work/_temp/Library/gggenomes/extdata/emales/emales-tirs.gff]
#> # A tibble: 12 × 4
#> file_id seq_id seq_desc length
#> <chr> <chr> <chr> <dbl>
#> 1 emales BVI_008A NA 26820
#> 2 emales BVI_069 NA 26808
#> 3 emales Cflag_017B NA 21311
#> 4 emales E4-10_086 NA 20642
#> 5 emales E4-10_112 NA 26856
#> 6 emales RCC970_016B NA 20152
#> 7 emales-tirs BVI_008A NA 26820
#> 8 emales-tirs BVI_069 NA 26808
#> 9 emales-tirs Cflag_017B NA 21311
#> 10 emales-tirs E4-10_086 NA 20642
#> 11 emales-tirs E4-10_112 NA 26856
#> 12 emales-tirs RCC970_016B NA 20152