mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
a19ae79b85
Cripple accepted tool input formats for many of the FASTQ tools to only allow only fastqsanger and fastqcssanger to be used.
111 lines
4.3 KiB
Python
111 lines
4.3 KiB
Python
#Dan Blankenberg
|
|
|
|
class fastaSequence( object ):
|
|
def __init__( self ):
|
|
self.identifier = None
|
|
self.sequence = '' #holds raw sequence string: no whitespace
|
|
def __len__( self ):
|
|
return len( self.sequence )
|
|
def __str__( self ):
|
|
return "%s\n%s\n" % ( self.identifier, self.sequence )
|
|
|
|
class fastaReader( object ):
|
|
def __init__( self, fh ):
|
|
self.file = fh
|
|
def close( self ):
|
|
return self.file.close()
|
|
def next( self ):
|
|
line = self.file.readline()
|
|
#remove header comment lines
|
|
while line and line.startswith( '#' ):
|
|
line = self.file.readline()
|
|
if not line:
|
|
raise StopIteration
|
|
assert line.startswith( '>' ), "FASTA headers must start with >"
|
|
rval = fastaSequence()
|
|
rval.identifier = line.strip()
|
|
offset = self.file.tell()
|
|
while True:
|
|
line = self.file.readline()
|
|
if not line or line.startswith( '>' ):
|
|
if line:
|
|
self.file.seek( offset ) #this causes sequence id lines to be read twice, once to determine previous sequence end and again when getting actual sequence; can we cache this to prevent it from being re-read?
|
|
return rval
|
|
#454 qual test data that was used has decimal scores that don't have trailing spaces
|
|
#so we'll need to parse and build these sequences not based upon de facto standards
|
|
#i.e. in a less than ideal fashion
|
|
line = line.rstrip()
|
|
if ' ' in rval.sequence or ' ' in line:
|
|
rval.sequence = "%s%s " % ( rval.sequence, line )
|
|
else:
|
|
rval.sequence += line
|
|
offset = self.file.tell()
|
|
def __iter__( self ):
|
|
while True:
|
|
yield self.next()
|
|
|
|
class fastaNamedReader( object ):
|
|
def __init__( self, fh ):
|
|
self.file = fh
|
|
self.reader = fastaReader( self.file )
|
|
self.offset_dict = {}
|
|
self.eof = False
|
|
def close( self ):
|
|
return self.file.close()
|
|
def get( self, sequence_id ):
|
|
if not isinstance( sequence_id, basestring ):
|
|
sequence_id = sequence_id.identifier
|
|
rval = None
|
|
if sequence_id in self.offset_dict:
|
|
initial_offset = self.file.tell()
|
|
seq_offset = self.offset_dict[ sequence_id ].pop( 0 )
|
|
if not self.offset_dict[ sequence_id ]:
|
|
del self.offset_dict[ sequence_id ]
|
|
self.file.seek( seq_offset )
|
|
rval = self.reader.next()
|
|
self.file.seek( initial_offset )
|
|
else:
|
|
while True:
|
|
offset = self.file.tell()
|
|
try:
|
|
fasta_seq = self.reader.next()
|
|
except StopIteration:
|
|
self.eof = True
|
|
break #eof, id not found, will return None
|
|
if fasta_seq.identifier == sequence_id:
|
|
rval = fasta_seq
|
|
break
|
|
else:
|
|
if fasta_seq.identifier not in self.offset_dict:
|
|
self.offset_dict[ fasta_seq.identifier ] = []
|
|
self.offset_dict[ fasta_seq.identifier ].append( offset )
|
|
return rval
|
|
def has_data( self ):
|
|
#returns a string representation of remaining data, or empty string (False) if no data remaining
|
|
eof = self.eof
|
|
count = 0
|
|
rval = ''
|
|
if self.offset_dict:
|
|
count = sum( map( len, self.offset_dict.values() ) )
|
|
if not eof:
|
|
offset = self.file.tell()
|
|
try:
|
|
fasta_seq = self.reader.next()
|
|
except StopIteration:
|
|
eof = True
|
|
self.file.seek( offset )
|
|
if count:
|
|
rval = "There were %i known sequences not utilized. " % count
|
|
if not eof:
|
|
rval = "%s%s" % ( rval, "An additional unknown number of sequences exist in the input that were not utilized." )
|
|
return rval
|
|
|
|
class fastaWriter( object ):
|
|
def __init__( self, fh ):
|
|
self.file = fh
|
|
def write( self, fastq_read ):
|
|
#this will include color space adapter base if applicable
|
|
self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) )
|
|
def close( self ):
|
|
return self.file.close()
|