fastqtools.readprocess package

Submodules

fastqtools.readprocess.readprocess module

class fastqtools.readprocess.readprocess.readprocess(read)[source]
autoadaptremove(flag)[source]
length(lenMin)[source]
nbase(percent)[source]
qual(q, percent)[source]
trim(head1, tail1, head2, tail2)[source]
umi(umis)[source]

fastqtools.readprocess.tools module

fastqtools.readprocess.tools.autocutadaptor(seq1, seq2)[source]
fastqtools.readprocess.tools.checkN(seq, percent)[source]
fastqtools.readprocess.tools.checking_adaptor(seq1, seq2, common, threadhold=0.95)[source]
fastqtools.readprocess.tools.checkqual(qual, q_thread, percent)[source]
fastqtools.readprocess.tools.checkumi(seq, umis)[source]
fastqtools.readprocess.tools.code2score(code)[source]
fastqtools.readprocess.tools.diffstr(str1, str2)[source]
class fastqtools.readprocess.tools.dnaseq[source]
static complent(seq)[source]
static reverse(seq)[source]
fastqtools.readprocess.tools.enlong_and_find_common(seq1, seq2, seed_choosed, mismatchMax=5)[source]

return best common sequences.

fastqtools.readprocess.tools.score2code(score)[source]
fastqtools.readprocess.tools.seeding(seq1, seq2, seed_len=10, seed_max=3, seed_step=1)[source]

find seed candidates return seeds and locus.

Module contents