[emboss-dev] Question about sequence input-output - Checked by AntiVir DEMO version

[Guy Bottu]

	Dear developers,

I just installed the patched versions of ajseqread.c and ajseqwrite.c in 
order to prepare for the new release of EMBL. I took the occasion to take 
a look at the supported formats for input and output and was a litlte 
surprised :
- for input the names "embl" and "em" support both the old and the new 
format. For writing "embl", "em" and "emblold" write in old format and 
"emblnew" writes in new format. Is that not a little bit confusing ?
- Worse is the following : for reading "ncbi" and "fasta" read NCBI fastA 
format, "pearson" reads standard fastA format. For writing "ncbi" writes 
NCBI fastA format and "pearson" and "fasta" write standard fastA format. 
I remember that a colleague of mine had troubles because of this. Should 
"fasta" not consistently have the same meaning and then preferably be 
synonymous of "pearson" ?
- I also noted that jackkinfernon, nexusnon and meganon are only 
supported for writing, not for reading, even if they are mentioned as 
input formats in 
http://emboss.sourceforge.net/docs/themes/SequenceFormats.html

	Comments ?

	Guy Bottu,
	BEN