diff --git a/libriboseq/libriboseq.pyx b/libriboseq/libriboseq.pyx index 7d381e0f7cde7201504bc7b801d39f53346eb266..db405d6739cab6f2cefb58c35ee5d8cad29c95d9 100755 --- a/libriboseq/libriboseq.pyx +++ b/libriboseq/libriboseq.pyx @@ -159,42 +159,42 @@ cdef bint crpf_has_good_psite(object isgood, str seq): def is_rpf29gooda(object isgood, str seq, int read_len): - """Return True if this is a RPF29goodA.""" + """RPF29goodA: 29 nt, good codon at the A site (positions 16-18)""" return cread_is_29nt(read_len) and crpf_has_good_asite(isgood, seq) def is_rpf29bada(object isgood, str seq, int read_len): - """Return True if this is a RPF29badA.""" + """RPF29badA: 29 nt, bad codon at the A site (positions 16-18)""" return cread_is_29nt(read_len) and not crpf_has_good_asite(isgood, seq) def is_rpf29goodp(object isgood, str seq, int read_len): - """Return True if this is a RPF29goodP.""" + """RPF29goodP: 29 nt, good codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and crpf_has_good_psite(isgood, seq) def is_rpf29badp(object isgood, str seq, int read_len): - """Return True if this is a RPF29badP.""" + """RPF29badP: 29 nt, bad codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and not crpf_has_good_psite(isgood, seq) def is_rpf29goodagoodp(object isgood, str seq, int read_len): - """Return True if this is a RPF29goodAgoodP.""" + """RPF29goodAgoodP: 29 nt, good codon at the A site (positions 16-18) and good codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and crpf_has_good_asite(isgood, seq) and crpf_has_good_psite(isgood, seq) def is_rpf29goodabadp(object isgood, str seq, int read_len): - """Return True if this is a RPF29goodAbadP.""" + """RPF29goodAbadP: 29 nt, good codon at the A site (positions 16-18) and bad codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and crpf_has_good_asite(isgood, seq) and (not crpf_has_good_psite(isgood, seq)) def is_rpf29badagoodp(object isgood, str seq, int read_len): - """Return True if this is a RPF29badAgoodP.""" + """RPF29badAgoodP: 29 nt, bad codon at the A site (positions 16-18) and good codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and (not crpf_has_good_asite(isgood, seq)) and crpf_has_good_psite(isgood, seq) def is_rpf29badabadp(object isgood, str seq, int read_len): - """Return True if this is a RPF29badAbadP.""" + """RPF29badAbadP: 29 nt, bad codon at the A site (positions 16-18) and bad codon at the P site (positions 13-15)""" return cread_is_29nt(read_len) and (not crpf_has_good_asite(isgood, seq)) and (not crpf_has_good_psite(isgood, seq)) @@ -213,6 +213,7 @@ RPF2IS_FUN = { def make_fq_filter(str rpf_type, object isgood): if rpf_type == "RPF29": def fq_filter(fq_triplet): + """Reads of length 29 are called RPF29.""" (_, seq, _) = fq_triplet return cread_is_29nt(len(seq)) else: