add GFF

jdieramon · Apr 7, 2023 · f295442 · f295442
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diff --git a/dat/Saccharomyces_cerevisiae_genome.gff3 b/dat/Saccharomyces_cerevisiae_genome.gff3
diff --git a/genomics/GFF.Rmd b/genomics/GFF.Rmd
@@ -0,0 +1,82 @@
+---
+title: "GFF"
+author: "Jose V. Die"
+date: "4/7/2023"
+output: 
+  html_document:
+    keep_md: true
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## GFF
+
+The General Feature Format ([GFF](https://www.ensembl.org/info/website/upload/gff.html)) file has nine columns:  
+
+
+| colname | description |
+|---|---|
+| seqname | The name of the sequence; must be a chromosome or scaffold. |
+| source | The program that generated this feature. |
+| feature | The name of this type of feature, e.g. "CDS", "start_codon", "stop_codon", and "exon" |
+| start | The starting position of the feature in the sequence; the first base is numbered 1. |
+| end | The ending position of the feature (inclusive). |
+| score | A score between 0 and 1000. |
+| strand | Valid entries include "+", "-", or ".". |
+| frame | If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be ".". |
+
+Dependencies
+```{r dependencies, message=FALSE}
+library(rtracklayer)
+
+```
+
+### Load GFF file 
+```{r}
+gff_file <- "../dat/Saccharomyces_cerevisiae_genome.gff3"
+
+```
+Available molecular features in the GFF file 
+
+```{r}
+gff_all = import.gff(con = gff_file ,
+                      colnames = c("type", "mycolums"))
+table(gff_all$type)
+```
+
+Load gene models from the GFF file. 
+```{r}
+gff_chromosome = import.gff(con = gff_file ,
+                     feature.type = "chromosome",
+                     colnames = c("type", "mycolums"))
+
+gff_gene = import.gff(con = gff_file ,
+                     feature.type = "gene",
+                     colnames = c("type", "mycolums"))
+
+gff_exon = import.gff(con = gff_file ,
+                     feature.type = "exon",
+                     colnames = c("type", "mycolums"))
+```
+
+Look the data
+```{r}
+gff_chromosome
+
+gff_gene
+
+gff_exon
+
+```
+
+Genes on chr 'I' and strand 'forward'
+```{r}
+gff_gene[seqnames(gff_gene) == "I" & strand(gff_gene) == "+"]
+```
+
+
+https://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/GenomicRanges/doc/GenomicRangesHOWTOs.pdf
+
+
diff --git a/genomics/GFF.md b/genomics/GFF.md
@@ -0,0 +1,175 @@
+---
+title: "GFF"
+author: "Jose V. Die"
+date: "4/7/2023"
+output: 
+  html_document:
+    keep_md: true
+---
+
+
+
+## GFF
+
+The General Feature Format ([GFF](https://www.ensembl.org/info/website/upload/gff.html)) file has nine columns:  
+
+
+| colname | description |
+|---|---|
+| seqname | The name of the sequence; must be a chromosome or scaffold. |
+| source | The program that generated this feature. |
+| feature | The name of this type of feature, e.g. "CDS", "start_codon", "stop_codon", and "exon" |
+| start | The starting position of the feature in the sequence; the first base is numbered 1. |
+| end | The ending position of the feature (inclusive). |
+| score | A score between 0 and 1000. |
+| strand | Valid entries include "+", "-", or ".". |
+| frame | If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be ".". |
+
+Dependencies
+
+```r
+library(rtracklayer)
+```
+
+### Load GFF file 
+
+```r
+gff_file <- "../dat/Saccharomyces_cerevisiae_genome.gff3"
+```
+Available molecular features in the GFF file 
+
+
+```r
+gff_all = import.gff(con = gff_file ,
+                      colnames = c("type", "mycolums"))
+table(gff_all$type)
+```
+
+```
+## 
+##                chromosome                      gene                      mRNA 
+##                        17                      6600                      6600 
+##                      exon                       CDS                ncRNA_gene 
+##                      7507                      6913                       424 
+##                     ncRNA                      tRNA                    snoRNA 
+##                        18                       299                        77 
+## transposable_element_gene      transposable_element                pseudogene 
+##                        91                        91                        12 
+##    pseudogenic_transcript                     snRNA            five_prime_UTR 
+##                        12                         6                         4 
+##                      rRNA 
+##                        24
+```
+
+Load gene models from the GFF file. 
+
+```r
+gff_chromosome = import.gff(con = gff_file ,
+                     feature.type = "chromosome",
+                     colnames = c("type", "mycolums"))
+
+gff_gene = import.gff(con = gff_file ,
+                     feature.type = "gene",
+                     colnames = c("type", "mycolums"))
+
+gff_exon = import.gff(con = gff_file ,
+                     feature.type = "exon",
+                     colnames = c("type", "mycolums"))
+```
+
+Look the data
+
+```r
+gff_chromosome
+```
+
+```
+## GRanges object with 17 ranges and 2 metadata columns:
+##        seqnames    ranges strand |       type    mycolums
+##           <Rle> <IRanges>  <Rle> |   <factor> <character>
+##    [1]        I  1-230218      * | chromosome        <NA>
+##    [2]       II  1-813184      * | chromosome        <NA>
+##    [3]      III  1-316620      * | chromosome        <NA>
+##    [4]       IV 1-1531933      * | chromosome        <NA>
+##    [5]       IX  1-439888      * | chromosome        <NA>
+##    ...      ...       ...    ... .        ...         ...
+##   [13]      XII 1-1078177      * | chromosome        <NA>
+##   [14]     XIII  1-924431      * | chromosome        <NA>
+##   [15]      XIV  1-784333      * | chromosome        <NA>
+##   [16]       XV 1-1091291      * | chromosome        <NA>
+##   [17]      XVI  1-948066      * | chromosome        <NA>
+##   -------
+##   seqinfo: 17 sequences from an unspecified genome; no seqlengths
+```
+
+```r
+gff_gene
+```
+
+```
+## GRanges object with 6600 ranges and 2 metadata columns:
+##          seqnames        ranges strand |     type    mycolums
+##             <Rle>     <IRanges>  <Rle> | <factor> <character>
+##      [1]        I       335-649      + |     gene        <NA>
+##      [2]        I       538-792      + |     gene        <NA>
+##      [3]        I     1807-2169      - |     gene        <NA>
+##      [4]        I     2480-2707      + |     gene        <NA>
+##      [5]        I     7235-9016      - |     gene        <NA>
+##      ...      ...           ...    ... .      ...         ...
+##   [6596]      XVI 939922-941136      + |     gene        <NA>
+##   [6597]      XVI 943032-943896      + |     gene        <NA>
+##   [6598]      XVI 943880-944188      + |     gene        <NA>
+##   [6599]      XVI 944603-947701      + |     gene        <NA>
+##   [6600]      XVI 946856-947338      - |     gene        <NA>
+##   -------
+##   seqinfo: 17 sequences from an unspecified genome; no seqlengths
+```
+
+```r
+gff_exon
+```
+
+```
+## GRanges object with 7507 ranges and 2 metadata columns:
+##          seqnames        ranges strand |     type    mycolums
+##             <Rle>     <IRanges>  <Rle> | <factor> <character>
+##      [1]        I       335-649      + |     exon        <NA>
+##      [2]        I       538-792      + |     exon        <NA>
+##      [3]        I     1807-2169      - |     exon        <NA>
+##      [4]        I     2480-2707      + |     exon        <NA>
+##      [5]        I     7235-9016      - |     exon        <NA>
+##      ...      ...           ...    ... .      ...         ...
+##   [7503]      XVI 943032-943050      + |     exon        <NA>
+##   [7504]      XVI 943199-943896      + |     exon        <NA>
+##   [7505]      XVI 943880-944188      + |     exon        <NA>
+##   [7506]      XVI 944603-947701      + |     exon        <NA>
+##   [7507]      XVI 946856-947338      - |     exon        <NA>
+##   -------
+##   seqinfo: 17 sequences from an unspecified genome; no seqlengths
+```
+
+Genes on chr 'I' and strand 'forward'
+
+```r
+gff_gene[seqnames(gff_gene) == "I" & strand(gff_gene) == "+"]
+```
+
+```
+## GRanges object with 60 ranges and 2 metadata columns:
+##        seqnames        ranges strand |     type    mycolums
+##           <Rle>     <IRanges>  <Rle> | <factor> <character>
+##    [1]        I       335-649      + |     gene        <NA>
+##    [2]        I       538-792      + |     gene        <NA>
+##    [3]        I     2480-2707      + |     gene        <NA>
+##    [4]        I   10091-10399      + |     gene        <NA>
+##    [5]        I   12046-12426      + |     gene        <NA>
+##    ...      ...           ...    ... .      ...         ...
+##   [56]        I 221049-221660      + |     gene        <NA>
+##   [57]        I 222406-222891      + |     gene        <NA>
+##   [58]        I 225460-226863      + |     gene        <NA>
+##   [59]        I 227742-228953      + |     gene        <NA>
+##   [60]        I 228844-229317      + |     gene        <NA>
+##   -------
+##   seqinfo: 17 sequences from an unspecified genome; no seqlengths
+```
+
diff --git a/genomics.R → genomics/genomics.R b/genomics.R → genomics/genomics.R
diff --git a/mkFastaFiles.sh → genomics/mkFastaFiles.sh b/mkFastaFiles.sh → genomics/mkFastaFiles.sh
diff --git a/promoter.md → genomics/promoter.md b/promoter.md → genomics/promoter.md
diff --git a/vcd.Rmd → genomics/vcd.Rmd b/vcd.Rmd → genomics/vcd.Rmd