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more functional minimap2.py; added categories

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Heng Li
2017-09-17 17:06:39 -04:00
parent 0b660c70e2
commit cf93e5c0a1
5 changed files with 43 additions and 7 deletions
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5
python/mappy.pyx
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@@ -67,8 +67,11 @@ cdef class Alignment:
else: strand = '?'
if self._is_primary != 0: tp = 'tp:A:P'
else: tp = 'tp:A:S'
if self._trans_strand > 0: ts = 'ts:A:+'
elif self._trans_strand < 0: ts = 'ts:A:-'
else: ts = 'ts:A:.'
return "\t".join([str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
str(self._blen - self._NM), str(self._blen), str(self._mapq), "NM:i:" + str(self._NM), tp, "cg:Z:" + self.cigar_str])
str(self._blen - self._NM), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
cdef class ThreadBuffer:
cdef cmappy.mm_tbuf_t *_b

23
python/minimap2.py
View File

@@ -4,11 +4,28 @@ import sys, getopt
import mappy as mp
def main(argv):
opts, args = getopt.getopt(argv[1:], "")
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:")
if len(args) < 2:
print("Usage: minimap2.py <ref.fa>|<ref.mmi> <query.fq>")
print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
print("Options:")
print(" -x STR preset: sr, map-pb, map-ont, asm5, asm10 or splice")
print(" -n INT mininum number of minimizers")
print(" -m INT mininum chaining score")
print(" -k INT k-mer length")
print(" -w INT minimizer window length")
print(" -r INT band width")
sys.exit(1)
a = mp.Aligner(args[0]) # load/build index
preset, min_cnt, min_sc, k, w, bw = None, None, None, None, None, None
for opt, arg in opts:
if opt == '-x': preset = arg
elif opt == '-n': min_cnt = int(arg)
elif opt == '-m': min_chain_score = int(arg)
elif opt == '-r': bw = int(arg)
elif opt == '-k': k = int(arg)
elif opt == '-w': w = int(arg)
a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
for h in a.map(seq): # traverse hits