[Seqinr-commits] r1951 - pkg/man

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

Author: jeanlobry
Date: 2016-06-21 10:10:03 +0200 (Tue, 21 Jun 2016)
New Revision: 1951

Modified:
   pkg/man/read.fasta.Rd
Log:
adding doc about fasta file extension names

Modified: pkg/man/read.fasta.Rd
===================================================================
--- pkg/man/read.fasta.Rd	2016-06-17 19:50:20 UTC (rev 1950)
+++ pkg/man/read.fasta.Rd	2016-06-21 08:10:03 UTC (rev 1951)
@@ -54,6 +54,13 @@
   are ignored, as in the original FASTA program (Pearson and Lipman 1988).
   The sequence name is just after the '>' up to the next space ' ' character,
   trailling infos are ignored for the name but saved in the annotations.
+  
+  There is no standard file extension name for a FASTA file. Commonly
+  found values are .fasta, .fas, .fa and .seq for generic FASTA files.
+  More specific file extension names are also used for fasta sequence
+  alignement (.fsa), fasta nucleic acid (.fna), fasta functional
+  nucleotide (.ffn), fasta amino acid (.faa), multiple protein
+  fasta (.mpfa), fasta RNA non-coding (.frn).
 
   The MAQ fasta binary format was introduced in seqinR 1.1-7 and has not
   been extensively tested. This format is used in the MAQ (Mapping and 
@@ -165,8 +172,8 @@
   bfavers <- read.fasta(bfafile, as.string = TRUE, set.att = FALSE, bfa = TRUE,
     endian = "little", sizeof.longlong = 8)
   if(!identical(original, bfavers)){
-     warning(paste("trouble reading bfa file with endian =", .Platform$endian, 
-    "and sizeof.longlong =", .Machine$sizeof.longlong))
+     warning(paste("trouble reading bfa file on a platform with endian =", 
+     .Platform$endian, "and sizeof.longlong =", .Machine$sizeof.longlong))
   }
   }
 }