def test_tabs2genetrack(self):
"Testing bed2genetrack transformation"
from genetrack.scripts import tabs2genetrack
inpfile = conf.testdata('short-data.bed', verify=True)
outfile = conf.tempdata('short-data.genetrack')
tabs2genetrack.transform(inpfile, outfile, format='BED')
def transform(inpname, outname, format, shift=0, index=False, options=None):
"""
Transforms reads stored in bedfile to a genetrack input file.
Requires at least 6 bed columns to access the strand.
"""
# detect file formats
if format == "BED":
CHROM, START, END, STRAND = 0, 1, 2, 5
elif format == "GFF":
CHROM, START, END, STRAND = 0, 3, 4, 6
else:
raise Exception('Invalid file format' % format)
# two sanity checks, one day someone will thank me
if format == 'BED' and inpname.endswith('gff'):
raise Exception('BED format on a gff file?')
if format == 'GFF' and inpname.endswith('bed'):
raise Exception('GFF format on a bed file?')
# find the basename of the outputname
basename = os.path.basename(outname)
# two files store intermediate results
flat = conf.tempdata( '%s.flat' % basename )
sorted = conf.tempdata( '%s.sorted' % basename )
# check for track information on first line,
# much faster this way than conditional checking on each line
fp = file(inpname, 'rU')
first = fp.readline()
fp.close()
# create the reader
reader = csv.reader(file(inpname, 'rU'), delimiter='\t')
# skip if trackline exists
if first.startswith == 'track':
reader.next()
# unwind the comments
list(takewhile(lambda x: x[0].startswith('#'), reader))
# copious timing info for those who enjoy these
timer, full = util.Timer(), util.Timer()
logger.debug("parsing '%s'" % inpname)
logger.debug("output to '%s'" % outname)
# create the unsorted output file and apply corrections
logger.debug("unsorted flat file '%s'" % flat)
fp = file(flat, 'wt')
for linec, row in enumerate(reader):
try:
chrom, start, end, strand = row[CHROM], row[START], row[END], row[STRAND]
except Exception, exc:
first = row[0][0]
# may be hitting the end of the file with other comments
if first == '>':
break # hit the sequence content of the gff file
elif first == '#':
continue # hit upon some comments
else:
logger.error(row)
raise Exception(exc)
if strand == '+':
# on forward strand, 5' is at start
idx = int(start) + shift
fwd, rev, val = 1, 0, 1
elif strand == '-':
# on reverse strand, 5' is at end
idx = int(end) - shift
fwd, rev, val = 0, 1, 1
else:
# no strand specified, generate interval centers
idx = (int(start)+int(end))/2
fwd, rev, val = 0, 0, 1
# it is essential be able to sort the index as a string!
fp.write('%s\t%012d\t%s\t%s\t%s\n' % (chrom, idx, fwd, rev, val))
def bedfile(inpfile):
basename = os.path.basename(inpfile)
outfile = conf.tempdata('%s.genetrack' % basename)
bed2genetrack.transform(inpfile, outfile)
def bedfile(inpfile):
basename = os.path.basename(inpfile)
outfile = conf.tempdata('%s.genetrack' % basename)
bed2genetrack.transform(inpfile, outfile)