read.phy: Read phylip file

In seqRFLP: Simulation and visualization of restriction enzyme cutting pattern from DNA sequences.

Description

Function to read phylip file.

Usage

read.phy(fil = NULL)

Arguments

fil	A character string naming the file path.

Details

Read phylip file from a specified file path (usually local machine) or URL.

Value

Returns a nexus "nxs" object stored as a vector of character strings.

Note

To be added.

Author(s)

Jinlong zhang [e-mail]

References

None.

See Also

See Also read.nxs, read.fasta for importing data from other data types.

Examples

##### read.phy() example
data(fil.phy)
writeLines(fil.phy, "example.phy")
phy <- read.phy("example.phy")
as.fasta(phy)
unlink("example.phy")

Example output

 [1] ">006_ITS1F"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [2] "TAGGTGAACCTGCGGAAGGATCATTATTGAACGAAAAGGGTGGCAAGGCTGTCGCTGGCTTGAATGAGCATGTGCACGTCTTTTGCTGCTTATTTCATTCTACTTCCACCTGTGCACTTTTTGTAGACACTTGGGAATGAGAGGTTGAATCAATTGACCTCTTGATAGTGAAAAAGTCTGGGTGTCTATGCATTTTTTATATACACAGTTGCATGTCTATAGAATGATGTTGTAGGCTTTTTTGCAAGCCTTTAAATTATAAAGTACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCTGAGGAGCATGCCTGTTTGAGTGTCATTAAGTATCTCAAAAGCTTATGCCTATTTTGTGGCATGGGACTTTTGGACAATGGGAGTTGCCGGTCACTGACAAAAGTGGTGGGCTCTTCTGAAAAGTATTAGTTGAGGAGCTTTGCACTCTATTGGTGTGATAGATTATCTATGCCAGGAGATGCTTTATGATCCTCTGCTGTCTAACCGTCTTTATTGGACAAACATGATGAACTTGACCTCAAATCAGGTAGGACTACCCGCTG"
 [3] ">006_ITS4_r"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
 [4] "TAGGTGAACCTGCGGAAGGATCATTATTGAACGAAAAGGGTGGCAAGGCTGTCGCTGGCTTGAATGAGCATGTGCACGTCTTTTGCTGCTTATTTCATTCTACTTCCACCTGTGCACTTTTTGTAGACACTTGGGAATGAGAGGTTGAATCAATTGACCTCTTGATAGTGAAAAAGTCTGGGTGTCTATGCATTTTTTATATACACAGTTGCATGTCTATAGAATGATGTTGTAGGCTTTTTTGCAAGCCTTTAAATTATAAAGTACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCTGAGGAGCATGCCTGTTTGAGTGTCATTAAGTATCTCAAAAGCTTATGCCTATTTTGTGGCATGGGACTTTTGGACAATGGGAGTTGCCGGTCACTGACAAAAGTGGTGGGCTCTTCTGAAAAGTATTAGTTGAGGAGCTTTGCACTCTATTGGTGTGATAGATTATCTATGCCAGGAGATGCTTTATGATCCTCTGCTGTCTAACCGTCTTTATTGGACAAACATGATGAACTGACCTCAAATCAGGTAGGA"           
 [5] ">003_ITS1F"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
 [6] "TAGGTGAACCTGCGGAAGGATCATTATTGAATAATGTCTGGCAGGAGGCTGTTGCTGGCCCAATAATGTGGCATGTGCACGCCTCTATAAAAGTCAGTTTTGAGTTACATTTTCCTGTGCATTTTTGTAGACACTTTGGATTGAGGAACTGTGTTGGTTTCTTGCTGTGAATATCAAGGTGTCTATGCTTTTTAATCAATACAAAGCATGTATCAGAATGGTTATTGATAATGAATAAAGTTGAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTAGTATTCTGAGGAGCATGCCTGTTTGAGTGTCATTAAATTCTCAAAATCCTCTCTGTTTGTGAGGCATTTTGGACATTGGGAGTTGCAGGTTTATGAAGCCAGCTCTCCTCAAATGAATTAGCAGGGAAATATGGGAATTTCTCCGTTGGTGTGATAAACTGTTTACACCATGAAATGAAGTCCCTGTACAATCTCTACTTTCTAAAGCATTTCTGTCCTAGAGATAGTAATGGGCTGGTTTGGTTGACTTGACCTCAAATCAGGTAGGGGTACCCGCTG"          
 [7] ">003_ITS4_r"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
 [8] "TAGGTGAACCTGCGGAAGGATCATTATTGAATAATGTCTGGCAGGAGGCTGTTGCTGGCCCAATAATGTGGCATGTGCACGCCTCTATAAAAGTCAGTTTTGAGTTACATTTTCCTGTGCATTTTTGTAGACACTTTGGATTGAGGAACTGTGTTGGTTTCTTGCTGTGAATATCAAGGTGTCTATGCTTTTTAATCAATACAAAGCATGTATCAGAATGGTTATTGATAATGAATAAAGTTGAATACAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTAGTATTCTGAGGAGCATGCCTGTTTGAGTGTCATTAAATTCTCAAAATCCTCTCTGTTTGTGAGGCATTTTGGACATTGGGAGTTGCAGGTTTATGAAGCCAGCTCTCCTCAAATGAATTAGCAGGGAAATATGGGAATTTCTCCGTTGGTGTGATAAACTGTTTACACCATGAAATGAAGTCCCTGTACAATCTCTACTTTCTAAAGCATTTCTGTCCTAGAGATAGTAATGGGCTGGTTTGGTTGACTTGACCTCAAATCAGGTA"                       
 [9] ">004_ITS1F"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[10] "TAGGTGAACCTGCGGAAGGATCATTATTGAATGCAGCCTTGATGGGTTGTCGCTGGCTCTAAACCTGAGCATGTGCACGCCTGTCTTGACTTCTATTCATCCACCTGTGCACCTTTTGTAGTCTTTTTGGGGGCTGGGGAAGCTGGCAGCTCAGGCTGTTGGATTGAACCTCCCACTTGGGGCTATGTTCTTATCATATACCATTTAGAATGTAACAGAATGTTGTCAATGGGCACTCTGTGGCCTATATGAAAAACTATACAACTTTCAGCAACGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTATATTCTCAACTCCACCAGCTTTTGTGGCTGGCTCTTGGAGATTGGATGTGGAGGCTTTGCTGGCCCTTGGTCAGCTCCTCTGAAATACATTAGCGGAACCGTTTGCGATCCGTCACAGGTGTGATAATTATCTACGCCAGTGGGTTGCTCTCTGTCTGTTCAGCTCATAATTGTCCTGGAACATGGACAAACTATAATGAACGTTTGACCTCAAATCAGGTAGGACTACCCGCTG"    
[11] ">004_ITS4_r"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
[12] "TAGGTGAACCTGCGGAAGGATCATTATTGAATGCAGCCTTGATGGGTTGTCGCTGGCTCTAAACCTGAGCATGTGCACGCCTGTCTTGACTTCTATTCATCCACCTGTGCACCTTTTGTAGTCTTTTTGGGGGCTGGGGAAGCTGGCAGCTCAGGCTGTTGGATTGAACCTCCCACTTGGGGCTATGTTCTTATCATATACCATTTAGAATGTAACAGAATGTTGTCAATGGGCACTCTGTGGCCTATATGAAAAACTATACAACTTTCAGCAACGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTATATTCTCAACTCCACCAGCTTTTGTGGCTGGCTCTTGGAGATTGGATGTGGAGGCTTTGCTGGCCCTTGGTCAGCTCCTCTGAAATACATTAGCGGAACCGTTTGCGATCCGTCACAGGTGTGATAATTATCTACGCCAGTGGGTTGCTCTCTGTCTGTTCAGCTCATAATTGTCCTGGAACATGGACAAACTATAATGAACGTTTGACCTCAAATCAGGTAGGA"              
[13] ">002_ITS1F"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[14] "TAGGTGAACCTGCGGAAGGATCATTATCGAACGAAACACTTCTGGCTTTATGCTGCTGTGTTGGCTGTTTGGGCAATGTGCACGTAGCTCTGGTCGGTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCAGTGTCTATGATATTTGTTACACACACATTGATGTTAGTTGGCATGTTGACATATATATAATAAATATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGCGAAATGTGATAAGTAATGTGAATTGCAGAATCCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAAACTATCAAAACACTTTTGCTTTTGTCGAAGTGTTTTGGACTTTGGGAGTGCTGGTCTCTTTTTGAGCCGGCTCTCCTCAAAAGCATTGCTTTGGAGACCATCAGCGTGATAATTTTATGTTTATGCCGCTGGCTTCTCCTTCTGTCCCTTTTGACCTCAAATCAGGTAGGACTACCCGCTGAACTTAAGCATATC"                                                                                                  
[15] ">002_ITS4_r"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
[16] "TAGGTGAACCTGCGGAAGGATCATTATCGAACGAAACACTTCTGGCTTTATGCTGCTGTGCTGGCTGTTTGGGCAATGTGCACGTAGCTCTGGTCGGTTGTTTCTTCTGTTCCACCTGTGCACTGCCTGTAGACACTCAGTGTCTATGATATTTGTTACACACACATTGATGTTAGTTGGCATGTTGACATATATATAATAAATATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACACAGCGAAATGTGATAAGTAATGTGAATTGCAGAATCCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAAACTATCAAAACACTTTTGCTTTTGTCGAAGTGTTTTGGACTTTGGGAGTGCTGGTCTCTTTTTGAGCCGGCTCTCCTCAAAAGCATTGCTTTGGAGACCATCAGCGTGATAATTTTATGTTTATGCCGCTGGCTTCTCCTTCTGTCCCTTTGACCTCAAATCAGGTA"                                                                                                                              
[17] ">001_ITS1F"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
[18] "TAGGTGAACCTGCGGAAGGATCATTATTGGAATTGAAACCCTTTGCAGGAGGCTGTTGCTGTGCCCCTTGGGTATGTGCACGTCTCTTGTGTGTTTCTTCCTTTATCTCCCACCTGTGCACTGATTTTGTAGACTACCTTTGGTGTCTATGATTATAATATACATCACACATTATATTGAATGTATTAGTTTTGAGGCCCTTTTGTGCCCCTTTATAAACAAATATACAACTTTCAACAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAATCTTCTCAAAACATTTAACTTTGTAATGTTTTGGATTTTGGGAGTCATTGCTGGCCGGTTGGAGTCAGCTCTCCTTAAAAGTAAATAGGATGGGAAAGGCCCTTTCTCCACTCATTTGGTGTGATAATTATCTATGCCAAGGGGGGGGGAGAGCTTTTTTTTCATCCCGGGCCCCAACACCTGTGTAGACCATTGTGACCACAACAGGGGGAAGAACCCCCTGAGATTATGAGCAT"                                     
[19] ">001_1_ITS1"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
[20] "TAGGTGAACCTGCGGAAGGATCATTATTGGAATTGAAACCCTTTGCAGGAGGCTGTTGCTGTGCCCCTTGGGTATGTGCACGTCTCTTGTGTGTTTCTTCCTTTATCTCCCACCTGTGCACTGATTTTGTAGACTACCTTTGGTGTCTATGATTATAATATACATCACACATTATATTGAATGTATTAGTTTTGAGGCCCTTTTGTGCGCCTTTATAAACAAATATACAACTTTCAACAATGGATCTCTTGGCTCTTGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAATCTTCTCAAAACATTTAACTTTGTAATGTTTTGGATTTTGGGAGTCATTGCTGGCCGGTTGGAGTCAGCTCTCCTTAAAAGTAAATAGGATGGGAAAGGCCCTTTCTCCACTCATTTGGTGTGATAATTATCTATGCCAAGGGGGGGGGAAAGGGTTTTTTTCGACCCGGGCCCCTACCCCCGTGTACACCATTTAGCCCTCATCTCGTGTGAGAACCCCCTGAAATTTTGAGTATATATAAACGG"                           
[21] ">001_1_ITS4"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
[22] "TCTCTGTGTCATATAGAAAAAAAAAAGGTATCACAATTTTCTATATGAGCACGCGGAAAAGTCTCTTTATGAGAATAGAACCCCTGCACAAGAGGGTGGCTGTGTGCCCCGGGGGTATGCACGTGTCTCGTGTGTGTTTTCTTTTTTATCTCCCCCGTGCGCAGAGATTTTGGAGACCCCTTGGGGTGTATGAGTTTATAATACACCTCACACTTTATATAAAATGTATTTTTTGAGGGCCCTTTTTGTGCCCTTATAAAAAAAAATACAAAATTTAACAAAAGATATCTTTGGTCTCGCGCAGAGAAAAAGAGCACAGAAAAATGATATAAAAAATGAGAATCGGAGAACACAGAGTCTCATAGTATTTTAGAACGTCTTTTGCTCTCTGGTATTTTGAGGGGCACACCCGTGTGAGAGTCTCAAAAATTTTCAAAACACATTAATTTTTAAAATTTTTGAGTTTGGGGGACACAGTGGGCCGGGGGGGGTGTCATCTCTCTAAAAAAAAAAATGGGAGGAAAAAGCCCTTTTCCCCTCTCATGGGGTGATAAAATTATATACCACAAGGGGGGGTGAAGGCTTTTTTCAAGTCCGGGTCCTAAACCCATGTAGACCAAATTGACCTCAAATCAGGTAGGA"                 
[23] ">001_ITS4"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
[24] "TCTCGGGCTCTTATAGAAAAAAAAAAGTTGTCACAATGTTTCTATATGAGAACGCGGAAAAGTCATAATAGTAGAATTGAAACCCTGCACAGGGGGGTGGTGGTGCCCCCCGGGGATATGCGCATGTCTCGTGTGTGTTTTCTTTTTTATCTCCCCCGTGCGCAGAGTTTGTGGAGACCCCCTGGGGTGTATGAGTTTATTATACACCTCACACTTTATATAAAGTGTTTTTTTTGAGGGCCCCTTTTGTGCCCTTTTAAAAAAAAATACAAAATTCTACACAAGATATCTTTGGTCTCGCGCAGAGAAAAAAAGCACAGAAAAATGATAAAAAAAATGAAAAGCGGAGAACACAGAGTCTCATAGTATTTTTAAGCGTCTTTTGCTCTCTGGTATTTTGAGGGGCACACCCGTGTGAGAGTCTCAATTATTTTCACAACACATTAATTTTTAAAATTTTTGATTTTGGGGGACACATTGGGCCGGGGGGGGTCTCATCTCTCTTAAAAAAAAAATAAGAGGAAAAAGCCCTTTTCCCCTCTCATGGGGTGAGAAAAATATATACCACAGGGGGGGGTGAAGGCTTTTTTCAAGTCCGGGTCCTAAACCCATGTAGACCAAATTGACCTCAAATCAGGTAGG"                 
attr(,"class")
[1] "fasta"

seqRFLP documentation built on May 2, 2019, 6:02 a.m.