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The vast majority of applications do not support ';' and if it was a
feature of the original format, it has been forgotten and ignored.
Making a program support it now would cause more problems than any
benefit would provide. If some programs support it and others do not,
then we suddenly would have more work to convert the two FASTA formats
between each other, and frankly that makes me want to abandon
bioinformatics altogether as "standard" file formats has been a huge
time sink in the field. FASTA in the form most programs support has
been the closest thing to a non-changing file format in bioinformatics,
which is sad.<br>
<br>
I do understand the desire to make a program as complaint with a
particular file format as possible. That is a good thing. In this case,
the file format has evolved since the original and has effectively
become a de facto standard. I would argue the de facto standard is the
right way to go in this case. If you or others disagree, what benefits
would it provide vs the amount of extra work and problems it would
create?<br>
<br>
-Brandon<br>
<br>
Bruce Southey wrote:
<blockquote
cite="midbbcd77d00707311908r5bfefe6ewdf6d595ec1461e99@mail.gmail.com"
type="cite">
<pre wrap="">Hi,
I know! I was surprised when I first found out about it.
The main source that I can find is the file FASTA.doc which is the
documentation for 'The FASTA program package' . So I am not sure if
you can get much more 'authoritative' than that. Consequently, every
package or reference that ignores the comment line is not implementing
the full FASTA spec and should be treated as such.
I found various versions of FASTA.doc online including:
<a class="moz-txt-link-freetext" href="http://molbio.unmc.edu/other-tools/fasta/fasta-help.html">http://molbio.unmc.edu/other-tools/fasta/fasta-help.html</a> (this one is
Release 2.0 1995)
In section 3.2. Sequence files:
"I have included several sample test files, *.AA. The first
line may begin with a '>' or ';' followed by a comment. The
text after ';' in other lines will be ignored. Spaces and
tabs (and anything else that is not an amino-acid code) are
ignored."
A similar example is:
<a class="moz-txt-link-freetext" href="http://www.psc.edu/general/software/packages/fasta/manual/fasta.html">http://www.psc.edu/general/software/packages/fasta/manual/fasta.html</a>
"The fasta3 programs use a standard text format sequence file. Lines
begin- ning with '>' or ';' are considered comments and ignored;
sequences can be upper or lower case, blanks,tabs and unrecognizable
characters are ignored."
Regards
Bruce
On 7/31/07, Andrew Dalke <a class="moz-txt-link-rfc2396E" href="mailto:dalke@dalkescientific.com"><dalke@dalkescientific.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Jul 31, 2007, at 9:05 PM, Bruce Southey wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I did notice that your FASTA section is incomplete because
you must address the comment part of the FASTA format (eg. see
<a class="moz-txt-link-freetext" href="http://en.wikipedia.org/wiki/Fasta_format">http://en.wikipedia.org/wiki/Fasta_format</a> ). Yeah, most programs and
people miss this but it is part of the format.
</pre>
</blockquote>
<pre wrap="">While I know it's in the Wikipedia page, and recall
mention of ;comments on a few other web pages, I have never
seen sequence libraries with those comments, nor have
I reviewed any source code which handles it. So I
removed that detail from the Wikipedia. In the
discussion section I'm pointing to this email, once it
gets in the bip archive.
I see no justification for having new code - and especially
not code meant for beginning programmers - support it when
the code cannot be tested against real-world data and
will never be used; because no new data sets will have
those comments.
Bioperl doesn't handle it. This is from Bio/SeqIO/fasta.pm
local $/ = "\n>";
return unless my $entry = $self->_readline;
chomp($entry);
...
$entry =~ s/^>//;
my ($top,$sequence) = split(/\n/,$entry,2);
defined $sequence && $sequence =~ s/>//g;
...
my ($id,$fulldesc);
if( $top =~ /^\s*(\S+)\s*(.*)/ ) {
($id,$fulldesc) = ($1,$2);
}
if (defined $id && $id eq '') {$id=$fulldesc;} # FIX incase no
space
# between > and
name \AE
defined $sequence && $sequence =~ s/\s//g; # Remove whitespace
which means it's certainly not found currently in the wild.
Gilbert's old readseq library doesn't handle it either. (The
code is in readPearson/endPearson in
<a class="moz-txt-link-freetext" href="http://iubio.bio.indiana.edu/soft/molbio/readseq/classic/src/">http://iubio.bio.indiana.edu/soft/molbio/readseq/classic/src/</a>
ureadseq.c
but not easily quotable because you have to know what
the "readLoop" and "getline" functions do.)
Together that means that for over 15 years two of the
most widely used sequence readers didn't handle this part
of the spec.
This exact topic was something I asked my students
a few years ago: Find three web pages which describe the
FASTA specification. Are any of them authoritative?
The Wikipedia page does not link to a formal spec.
Download the FASTA source and you'll find no spec. None
of the FASTA files distributed with the code contain a
leading ';'.
The only place I found was to look in the actual code.
This comes from for FASTA 35.1.5 : getseq.c
if (line[0]=='>') {
seq_format = FASTA_FORMAT;
#ifdef SUPERFAMNUM
...
#endif
if ((bp=(char *)strchr(line,'\n'))!=NULL) *bp='\0';
strncpy(seq_title,line+1,sizeof(seq_title));
seq_title[sizeof(seq_title)-1]='\0';
if ((bp=(char *)strchr(line,' '))!=NULL) *bp='\0';
strncpy(libstr,line+1,12);
libstr[12]='\0';
}
....
if (seq_format !=GCG_FORMAT)
while(fgets(line,sizeof(line),fptr)!=NULL) {
#ifdef PIRLIB
...
#endif
if (line[0]!='>'&& line[0]!=';') {
for (i=0; (n<maxs && rn < sstop)&&
((ic=qascii[line[i]&AAMASK])<EL); i++)
if (ic<NA && ++rn > sstart ) seq[n++]= ic;
if (ic == ES || rn > sstop) break;
}
}
The variable 'line' is 512 characters long. If this
is authoritative then this means that each sequence of
a FASTA record may be up to 511 characters, and no more.
I don't know what all that code is doing. It does
look like if the line is more than 512 characters long,
and the 512th character is a ">", then it will be
misinterpreted. But I would have to test it to find out.
So, ignore the Wikipedia entry. It was written by a
pedant. To respond in kind, the world parses "the
NCBI FASTA format" and not "the Pearson FASTA format" ;)
The NCBI FASTA format is at
<a class="moz-txt-link-freetext" href="http://www.ncbi.nlm.nih.gov/blast/fasta.shtml">http://www.ncbi.nlm.nih.gov/blast/fasta.shtml</a>
Andrew
<a class="moz-txt-link-abbreviated" href="mailto:dalke@dalkescientific.com">dalke@dalkescientific.com</a>
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