Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add capability for inputting full ForenSeq sequences (not run through UAS) #16

Merged
merged 18 commits into from
Apr 28, 2020
Merged

Add capability for inputting full ForenSeq sequences (not run through UAS) #16

Show file tree
Hide file tree
Changes from 7 commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
dd4f54c
Make sure all files are bundled correctly
standage Apr 2, 2020
40b4f8b
fixed style issues
Apr 23, 2020
fc444f7
Added full length sequence capability
Apr 23, 2020
4040bd2
Added PowerSeq cut points
Apr 23, 2020
34b18c7
Added PowerSeq option
Apr 24, 2020
066c45e
added test
Apr 24, 2020
6b022eb
Merge branch 'master' into fullsequences
standage Apr 24, 2020
22dca2d
Clean up conditional
standage Apr 24, 2020
9078590
minor fixes
Apr 24, 2020
197cccc
Refactor trimming
standage Apr 24, 2020
cc5f28a
More refactoring
standage Apr 24, 2020
7060c4c
Clean up makefile
standage Apr 24, 2020
567c340
Fix CI config
standage Apr 24, 2020
10e4689
added UAS annotate test
Apr 27, 2020
556ec5c
revised test
Apr 28, 2020
6e7fa72
Fix test by deleting output file before `lusstr annotate` writes to it
standage Apr 28, 2020
3558926
Rename variable to avoid conflicts with builtin function https://stac…
standage Apr 28, 2020
37ce9c2
added full seq test
Apr 28, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
86 changes: 63 additions & 23 deletions lusSTR/annot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,9 +116,9 @@ def rev_complement_anno(sequence):
'''
Function creates reverse complement of sequence

Sequences in which the UAS software output contains the sequence on the reverse strand require
translation of the sequence to the forward strand. This allows for consistency between both
loci and any outside analyses in which comparisons may be made.
Sequences in which the UAS software output contains the sequence on the reverse strand
require translation of the sequence to the forward strand. This allows for consistency
between both loci and any outside analyses in which comparisons may be made.
'''
complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
bases = list(sequence)
Expand All @@ -132,9 +132,9 @@ def rev_comp_forward_strand_bracket(rev_sequence, n, repeat_list, locusid, canno
'''
Function creates bracketed annotation for reverse complement sequences

Function is used to create the bracketed annotation for reverse complement sequences (i.e. the
forward strand). It calls additional functions depending on the locus and/or if the sequence
is a microvariant or not.
Function is used to create the bracketed annotation for reverse complement sequences (i.e
the forward strand). It calls additional functions depending on the locus and/or if the
sequence is a microvariant or not.
'''
if locusid in cannot_split_list:
if locusid == "D19S433":
Expand Down Expand Up @@ -591,6 +591,23 @@ def PentaD_annotation(sequence, no_of_repeat_bases, repeat_list):
return re.sub(" ", " ", final_string)


def full_seq_to_uas(full_seq, front, back):
'''
Function to trim full sequences to the UAS region.

It identifies the number of bases to remove from the 5' and 3' ends of the sequence to
trim to the UAS region. The downstream annotation, including length-based allele
designations, LUS, LUS+ and bracketed annotation is based on this region in the sequence.
'''
if front == 0:
seq_uas = full_seq[:-back]
elif back == 0:
seq_uas = full_seq[front:]
else:
seq_uas = full_seq[front:-back]
return seq_uas


def main(args):
cannot_split = [
"D19S433", "D6S1043", "TH01", "D21S11", "D1S1656", "D7S820", "D5S818", "D12S391",
Expand Down Expand Up @@ -619,32 +636,53 @@ def main(args):
lus = str_dict[locus]['LUS']
sec = str_dict[locus]['Sec']
tert = str_dict[locus]['Tert']
str_allele = traditional_str_allele(sequence, no_of_repeat_bases, no_of_sub_bases)
foren_5 = str_dict[locus]['Foren_5']
foren_3 = str_dict[locus]['Foren_3']
power_5 = str_dict[locus]['Power_5']
power_3 = str_dict[locus]['Power_3']
standage marked this conversation as resolved.
Show resolved Hide resolved
if args.uas:
uas_sequence = sequence
else:
if args.kit == "forenseq":
if str_dict[locus]['ReverseCompNeeded'] == "No":
uas_sequence = full_seq_to_uas(sequence, foren_5, foren_3)
else:
uas_from_full = full_seq_to_uas(sequence, foren_5, foren_3)
uas_sequence = rev_complement_anno(uas_from_full)
elif args.kit == "powerseq":
if str_dict[locus]['ReverseCompNeeded'] == "No":
uas_sequence = full_seq_to_uas(sequence, power_5, power_3)
else:
uas_from_full = full_seq_to_uas(sequence, power_5, power_3)
uas_sequence = rev_complement_anno(uas_from_full)
str_allele = traditional_str_allele(uas_sequence, no_of_repeat_bases, no_of_sub_bases)
if (
locus in cannot_split or
((len(sequence) % no_of_repeat_bases != 0) and locus not in must_split)
((len(uas_sequence) % no_of_repeat_bases != 0) and locus not in must_split)
):
standage marked this conversation as resolved.
Show resolved Hide resolved
if str_dict[locus]['ReverseCompNeeded'] == "Yes":
reverse_comp_sequence = rev_complement_anno(sequence)
reverse_comp_sequence = rev_complement_anno(uas_sequence)
print(reverse_comp_sequence)
standage marked this conversation as resolved.
Show resolved Hide resolved
forward_strand_bracketed_form = rev_comp_forward_strand_bracket(
reverse_comp_sequence, no_of_repeat_bases, repeats, locus, cannot_split
)
print(forward_strand_bracketed_form)
standage marked this conversation as resolved.
Show resolved Hide resolved
reverse_strand_bracketed_form = rev_comp_uas_output_bracket(
forward_strand_bracketed_form, no_of_repeat_bases
)
elif locus == "D21S11":
forward_strand_bracketed_form = D21_bracket(
sequence, no_of_split_bases, repeats
uas_sequence, no_of_split_bases, repeats
)
elif locus == "TH01" and (len(sequence) % no_of_repeat_bases != 0):
forward_strand_bracketed_form = TH01_annotation(sequence, repeats)
elif locus == "TH01" and (len(uas_sequence) % no_of_repeat_bases != 0):
forward_strand_bracketed_form = TH01_annotation(uas_sequence, repeats)
elif locus == "PentaD":
forward_strand_bracketed_form = PentaD_annotation(
sequence, no_of_repeat_bases, repeats
uas_sequence, no_of_repeat_bases, repeats
)
else:
forward_strand_bracketed_form = split_string(
sequence, no_of_repeat_bases, repeats
uas_sequence, no_of_repeat_bases, repeats
)
lus_final, sec_final, tert_final = lus_anno(
forward_strand_bracketed_form, lus, sec, tert, locus, str_allele
Expand All @@ -653,14 +691,14 @@ def main(args):
if locus == "D18S51":
if type(str_allele) == str:
forward_strand_bracketed_form = split_string(
sequence, no_of_repeat_bases, repeats
uas_sequence, no_of_repeat_bases, repeats
)
else:
forward_strand_bracketed_form = loci_need_split_anno(
sequence, no_of_repeat_bases
uas_sequence, no_of_repeat_bases
)
elif str_dict[locus]['ReverseCompNeeded'] == "Yes":
reverse_comp_sequence = rev_complement_anno(sequence)
reverse_comp_sequence = rev_complement_anno(uas_sequence)
forward_strand_bracketed_form = rev_comp_forward_strand_bracket(
reverse_comp_sequence, no_of_repeat_bases, repeats, locus, cannot_split
)
Expand All @@ -669,10 +707,12 @@ def main(args):
)
elif locus == "PentaD":
forward_strand_bracketed_form = PentaD_annotation(
sequence, no_of_repeat_bases, repeats
uas_sequence, no_of_repeat_bases, repeats
)
else:
forward_strand_bracketed_form = loci_need_split_anno(sequence, no_of_repeat_bases)
forward_strand_bracketed_form = loci_need_split_anno(
uas_sequence, no_of_repeat_bases
)
lus_final, sec_final, tert_final = lus_anno(
forward_strand_bracketed_form, lus, sec, tert, locus, str_allele
)
Expand All @@ -692,14 +732,14 @@ def main(args):
lus_plus = f"{str_allele}_{lus_final}_{sec_final}_{tert_final}"
if str_dict[locus]['ReverseCompNeeded'] == "Yes":
summary = [
sampleid, project, analysis, locus, sequence, reverse_comp_sequence, str_allele,
forward_strand_bracketed_form, reverse_strand_bracketed_form, lus_final_output,
lus_plus, reads
sampleid, project, analysis, locus, uas_sequence, reverse_comp_sequence,
str_allele, forward_strand_bracketed_form, reverse_strand_bracketed_form,
lus_final_output, lus_plus, reads
]
summary = '\t'.join(str(i) for i in summary)
else:
summary = [
sampleid, project, analysis, locus, sequence, sequence, str_allele,
sampleid, project, analysis, locus, uas_sequence, uas_sequence, str_allele,
forward_strand_bracketed_form, forward_strand_bracketed_form, lus_final_output,
lus_plus, reads
]
Expand Down
9 changes: 9 additions & 0 deletions lusSTR/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,15 @@ def annot_subparser(subparsers):
'input', help='sample(s) in CSV format; first four columns must be Locus, NumReads, '
'Sequence, SampleID; Optional last two columns can be Project and Analysis.'
)
cli.add_argument(
'--kit', choices=['forenseq', 'powerseq'], default='forenseq',
help='Kit used to develop sequences; only forenseq or powerseq accepted;'
'default = forenseq'
)
cli.add_argument(
'--uas', action='store_true',
help='Use if sequences have been run through the ForenSeq UAS.'
)


mains = {
Expand Down
Loading