def compile_refs( refs ):
'''
Compile all given refs into a single file to be indexed
@TODO -- Write tests
@param refs - Directory/file of fasta formatted files
@return path to concatted indexed reference file
'''
ref_files = []
ref_extensions = ('.fa', '.fasta', '.fna', '.fas')
if os.path.isdir( refs ):
logger.info( "Compiling and concatting refs inside of {}".format(refs) )
files = glob.glob( os.path.join( refs, '*' ) )
logger.debug( "All files inside of {}: {}".format( files, refs ) )
ref_files = [f for f in files if os.path.splitext(f)[1] in ref_extensions]
logger.debug( "Filtering files down to only files with extensions in {}".format(ref_extensions) )
logger.debug( "Filtered files to concat: {}".format( ref_files ) )
try:
seqio.concat_files( ref_files, 'reference.fa' )
except (OSError,IOError,ValueError) as e:
logger.error( "There was an error with the references in {}".format(refs) )
logger.error( str( e ) )
sys.exit(1)
return 'reference.fa'
else:
return refs
def compile_reads( reads, outputfile='reads.fastq' ):
'''
Compile all given reads from directory of reads or just return reads if it is fastq
If reads is sff file then convert to fastq
@param reads - Directory/file of .fastq or .sff
@param outputfile - File path of single fastq file output
@return fastq with all reads from reads
'''
if os.path.isdir( reads ):
reads = seqio.get_reads( reads )
elif isinstance( reads, str ):
# Single read file given
if os.path.splitext( reads )[1] == '.sff':
# Just convert the single reads
return seqio.sffs_to_fastq( [reads], outputfile )
else:
# Already fastq so nothing to do
# This is a bad assumption
return reads
# Empty read list
if not len( reads ):
return []
# Get only sff files to convert
sffs = fnmatch.filter( reads, '*.sff' )
tmpsfffastq = None
if len( sffs ):
tmpsfffastq = os.path.join(
os.path.dirname( outputfile ),
'sff.' + os.path.basename( outputfile )
)
logger.info( "Concatting and Converting {} to fastq".format(sffs) )
sfffastq = [seqio.sffs_to_fastq( sffs, tmpsfffastq )]
else:
sfffastq = []
fastqs = fnmatch.filter( reads, '*.fastq' )
# Concat fastq files and sff converted fastq files into
# outputfile
converts = fastqs + sfffastq
logger.info( "Concatting {} to {}".format(
converts, outputfile
)
)
seqio.concat_files( fastqs + sfffastq, outputfile )
if tmpsfffastq is not None:
os.unlink( tmpsfffastq )
return outputfile
