[adegenet-commits] r905 - in pkg: R inst/files man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2011-06-13 13:39:15 +0200 (Mon, 13 Jun 2011)
New Revision: 905

Added:
   pkg/inst/files/usflu.fasta
   pkg/man/fasta2genlight.Rd
Modified:
   pkg/R/import.R
   pkg/man/read.PLINK.Rd
   pkg/man/read.snp.Rd
Log:
fasta2genlight almost integrated - need to adapt the function to blanks in the alignments


Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R	2011-06-13 11:15:06 UTC (rev 904)
+++ pkg/R/import.R	2011-06-13 11:39:15 UTC (rev 905)
@@ -1034,7 +1034,7 @@
 ###########################
 ## Function fasta2genlight
 ###########################
-fasta2genlight <- function(file, quiet=FALSE, chunkSize=1000, saveNbAlleles=TRUE,
+fasta2genlight <- function(file, quiet=FALSE, chunkSize=1000, saveNbAlleles=FALSE,
                        multicore=require("multicore"), n.cores=NULL, ...){
     ## HANDLE ARGUMENTS ##
     ext <- .readExt(file)
@@ -1110,6 +1110,8 @@
 
 
     ## RE-READ DATA, CONVERT SNPs TO GENLIGHT ##
+    if(!quiet) cat("\n Extracting SNPs from the alignment... \n")
+
     ## initialize
     lines.to.skip <- 0
     COUNT <- 0 # used to count the nb reads

Added: pkg/inst/files/usflu.fasta
===================================================================
--- pkg/inst/files/usflu.fasta	                        (rev 0)
+++ pkg/inst/files/usflu.fasta	2011-06-13 11:39:15 UTC (rev 905)
@@ -0,0 +1,2400 @@
+> CY013200
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcagcaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
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+> CY013781
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+aggtgcaacatttgcatttga
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+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY013613
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+ggaaatgacaacagcacagcaacgctgtgcctaggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
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+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
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+> CY012160
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+> CY012272
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+> CY010988
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+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012288
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+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
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+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaattgcaggtttcatagaaaatggttgggag
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+gcagatcttaaaagcactcaagcagcaatcgaccaaatcgacgggaaactgaataggtta
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+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012568
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcgaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggctgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gtcgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY013016
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcggtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcatcgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacggaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcaccatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012480
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010748
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacatcatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaatgaaggc
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaactgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtccagaccctgggtgagg
+ggcatctccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgatcaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtggaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaatcaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcagcatttgcatttga
+> CY011528
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagactacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgttttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY017291
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctattcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatgggacc
+tgccccagatatgttaagcaaaacacactgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaatcaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012504
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaaggaaggc
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtatctccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaagctgaataggtta
+atcgagaaaacgaacgaaaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY009476
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaccaaagaaggc
+ttcaattggaccggagtcgctcaggatggaacaagctatgcttgcaaaaggggatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcggatgcacccattgacaactgcaattctgaatgcattactcca
+aatggaagcatttccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgaaggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaagaaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcattatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010028
+atgaagactattattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgcccagaatggaacaagctatgcttgcaaaaggagatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcaggataagcatatattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtggaaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY011128
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaccaaagaaggc
+ttcaattggactggagtcgctcaggatggaacaagctatgcttgcaaaaggggatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcggatgcacccattgacaactgcaattctgaatgcattactcca
+aatggaagcatttccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgaaggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaagaaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcattatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010036
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttcaaaaataaggaatgg
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 905