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#!/usr/bin/python3
"""
Read a maf and print the text as a fasta file, concatenating blocks. A
specific subset of species can be chosen.
usage %prog [options] species1,species2,... < maf_file > fasta_file
--fill="expression": Insert this between blocks
--wrap=columns: Wrap FASTA to this many columns
"""
import sys
from optparse import OptionParser
from bx.align import maf
def __main__():
# Parse command line arguments
parser = OptionParser()
parser.add_option("--fill", action="store", default=None, type="string", help="")
parser.add_option("--wrap", action="store", default=None, type="int", help="")
parser.add_option("--nowrap", action="store_true", default=False, dest="nowrap", help="")
(options, args) = parser.parse_args()
species = []
for arg in args:
species.extend(arg.split(","))
fill = ""
if options.fill:
fill = eval(options.fill)
wrap = 50
if options.wrap is not None:
wrap = options.wrap
elif options.nowrap:
wrap = 0
# create the concatenated sequences
texts = {}
for s in species:
texts[s] = []
maf_reader = maf.Reader(sys.stdin)
for m in maf_reader:
for s in species:
c = m.get_component_by_src_start(s)
if c:
texts[s].append(c.text)
else:
texts[s].append("-" * m.text_size)
for s in species:
print(">" + s)
print_n(fill.join(texts[s]), wrap)
def print_n(s, n, f=sys.stdout):
if n <= 0:
print(s, file=f)
else:
p = 0
while p < len(s):
print(s[p : min(p + n, len(s))], file=f)
p += n
if __name__ == "__main__":
__main__()
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