details: http://www.bx.psu.edu/hg/galaxy/rev/64506c9397e4 changeset: 1658:64506c9397e4 user: Dan Blankenberg dan@bx.psu.edu date: Thu Dec 11 16:00:06 2008 -0500 description: Update Fasta.sniff()
Rules for sniffing as True: We don't care about line length (other than empty lines). The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header. 'sequence data' here is loosely defined as non-empty lines which do not start with '>' This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data) Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta) This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta We will only check that the first purported sequence is correctly formatted.
1 file(s) affected in this change:
lib/galaxy/datatypes/sequence.py
diffs (83 lines):
diff -r 5c3736861e37 -r 64506c9397e4 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Dec 11 15:09:37 2008 -0500 +++ b/lib/galaxy/datatypes/sequence.py Thu Dec 11 16:00:06 2008 -0500 @@ -34,7 +34,7 @@ dataset.peek = data.get_file_peek( dataset.file_name ) dataset.blurb = data.nice_size( dataset.get_size() )
- def sniff(self, filename): + def sniff( self, filename ): """ Determines whether the file is in fasta format
@@ -42,7 +42,16 @@ The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 charcters
- For complete details see http://www.g2l.bio.uni-goettingen.de/blast/fastades.html + For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml + + Rules for sniffing as True: + We don't care about line length (other than empty lines). + The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header. + 'sequence data' here is loosely defined as non-empty lines which do not start with '>' + This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data) + Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta) + This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta + We will only check that the first purported sequence is correctly formatted.
>>> fname = get_test_fname( 'sequence.maf' ) >>> Fasta().sniff( fname ) @@ -51,34 +60,26 @@ >>> Fasta().sniff( fname ) True """ - headers = get_headers( filename, None ) - data_found = False + try: - if len(headers) > 1 and headers[0][0] and headers[0][0][0] == ">": - for i, l in enumerate( headers ): - line = l[0] - if i < 1: - continue - if line: - data_found = True - try: - int( line[0] ) - return False - except: - try: - elems = line.split() - int( elems[0] ) - return False - except: - return True - else: - return False - if data_found: - return True - else: - return False + fh = open( filename ) + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: #first non-empty line + if line.startswith( '>' ): + #The next line.strip() must not be '', nor startwith '>' + line = fh.readline().strip() + if line == '' or line.startswith( '>' ): + break + return True + else: + break #we found a non-empty line, but its not a fasta header except: - return False + pass + return False
class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """