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genomic / cdna coord conversion of upstream/downstream regions on NR transcripts #43

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genomic / cdna coord conversion of upstream/downstream regions on NR transcripts #43

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ae48f7c
Fix typo
Nov 15, 2017
af7c5ce
Add (some failing) unittests
Nov 16, 2017
24f5a50
Fix downstream/upstream cDNA errors when converting genomic coordinat…
Nov 16, 2017
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23 changes: 23 additions & 0 deletions pyhgvs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -527,6 +527,10 @@ def cdna_to_genomic_coord(transcript, coord):
if coord.coord < 0:
raise ValueError('CDNACoord cannot have a negative coord and '
'landmark CDNA_STOP_CODON')
if not transcript.is_coding:
if not transcript_strand:
pos = exons[-1].tx_position.chrom_start
return pos - coord.coord + 1
pos = find_stop_codon(exons, transcript.cds_position) + coord.coord
else:
raise ValueError('unknown CDNACoord landmark "%s"' % coord.landmark)
Expand Down Expand Up @@ -641,6 +645,25 @@ def genomic_to_cdna_coord(transcript, genomic_coord):
cdna_coord.coord == stop_codon and cdna_coord.offset > 0):
cdna_coord.coord -= stop_codon
cdna_coord.landmark = CDNA_STOP_CODON
else: # non coding
if strand == "+":
# Detect if position is after last exon.
if genomic_coord > exons[-1].chrom_end:
cdna_coord.coord = genomic_coord - exons[-1].chrom_end
cdna_coord.landmark = CDNA_STOP_CODON
else:
# Detect if position is before first exon.
if genomic_coord <= exons[0].chrom_start:
cdna_coord.coord -= 1
else: # neg strand
# Detect if position is after last exon.
if genomic_coord <= exons[-1].chrom_start:
cdna_coord.coord = exons[-1].chrom_start - genomic_coord + 1
cdna_coord.landmark = CDNA_STOP_CODON
else:
# Detect if position is before first exon.
if genomic_coord >= exons[0].chrom_end:
cdna_coord.coord -= 1

return cdna_coord

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22 changes: 21 additions & 1 deletion pyhgvs/tests/test_hgvs_names.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,7 @@ def test_invalid_coordinates():
]


# Test examples of coverting coordinates.
# Test examples of converting coordinates.
_convert_coords = [
# Positions near start codon.
('NM_000016.4', ('chr1', 76190473), CDNACoord(1)),
Expand Down Expand Up @@ -256,6 +256,24 @@ def test_invalid_coordinates():
('NM_000016.4', ('chr1', 76229354), CDNACoord(906, 0, CDNA_STOP_CODON)),
('NM_000016.4', ('chr1', 76229355), CDNACoord(907, 0, CDNA_STOP_CODON)),
('NM_000016.4', ('chr1', 76229356), CDNACoord(908, 0, CDNA_STOP_CODON)),

# NR, pos strand
('NR_002717.2', ('chr13', 70681609), CDNACoord(265, 0)), # exon 01
('NR_002717.2', ('chr13', 70713884), CDNACoord(1471, 0)), # exon 05
('NR_002717.2', ('chr13', 70682847), CDNACoord(529, 974)), # intron 01
('NR_002717.2', ('chr13', 70681344), CDNACoord(-1, 0)), # upstream
('NR_002717.2', ('chr13', 70681018), CDNACoord(-327, 0)), # upstream
('NR_002717.2', ('chr13', 70713886), CDNACoord(1, 0, CDNA_STOP_CODON)), # downstream
('NR_002717.2', ('chr13', 70714013), CDNACoord(128, 0, CDNA_STOP_CODON)), # downstream

# NR, neg strand
('NR_026759.1', ('chr9', 43033105), CDNACoord(208, 0)), # exon 01
('NR_026759.1', ('chr9', 43031289), CDNACoord(1106, 0)), # exon 04
('NR_026759.1', ('chr9', 43032642), CDNACoord(515, 156)), # intron 01
('NR_026759.1', ('chr9', 43033313), CDNACoord(-1, 0)), # upstream
('NR_026759.1', ('chr9', 43033387), CDNACoord(-75, 0)), # upstream
('NR_026759.1', ('chr9', 43027662), CDNACoord(1, 0, CDNA_STOP_CODON)), # downstream
('NR_026759.1', ('chr9', 43027589), CDNACoord(74, 0, CDNA_STOP_CODON)), # downstream
]


Expand Down Expand Up @@ -784,6 +802,8 @@ def test_invalid_coordinates():
'1440 NM_000038.5 chr5 + 112073555 112181936 112090587 112179823 16 112073555,112090569,112102022,112102885,112111325,112116486,112128142,112136975,112151191,112154662,112157592,112162804,112163625,112164552,112170647,112173249, 112073622,112090722,112102107,112103087,112111434,112116600,112128226,112137080,112151290,112155041,112157688,112162944,112163703,112164669,112170862,112181936, 0 APC cmpl cmpl -1,0,0,1,2,0,0,0,0,0,1,1,0,0,0,2,', # nopep8
'184 NM_000492.3 chr7 + 117120016 117308718 117120148 117307162 27 117120016,117144306,117149087,117170952,117174329,117175301,117176601,117180153,117182069,117188694,117199517,117227792,117230406,117231987,117234983,117242879,117243585,117246727,117250572,117251634,117254666,117267575,117282491,117292895,117304741,117305512,117306961, 117120201,117144417,117149196,117171168,117174419,117175465,117176727,117180400,117182162,117188877,117199709,117227887,117230493,117232711,117235112,117242917,117243836,117246807,117250723,117251862,117254767,117267824,117282647,117292985,117304914,117305618,117308718, 0 CFTR cmpl cmpl 0,2,2,0,0,0,2,2,0,0,0,0,2,2,0,0,2,1,0,1,1,0,0,0,0,2,0,', # nopep8
'1 ENST00000357654 chr17 - 41196311 41277387 41197694 41276113 23 41196311,41199659,41201137,41203079,41209068,41215349,41215890,41219624,41222944,41226347,41228504,41234420,41242960,41243451,41247862,41249260,41251791,41256138,41256884,41258472,41267742,41276033,41277287, 41197819,41199720,41201211,41203134,41209152,41215390,41215968,41219712,41223255,41226538,41228631,41234592,41243049,41246877,41247939,41249306,41251897,41256278,41256973,41258550,41267796,41276132,41277387, 0 ENSG00000012048 cmpl cmpl 1,0,1,0,0,1,1,0,1,2,1,0,1,1,2,1,0,1,2,2,2,0,-1,', # nopep8
'1124 NR_002717.2 chr13 + 70681344 70713885 70713885 70713885 5 70681344,70689272,70703915,70704809,70713372, 70681873,70689430,70704016,70704980,70713885, 0 ATXN8OS unk unk -1,-1,-1,-1,-1,', # nopep8
'913 NR_026759.1 chr9 - 43027662 43033312 43033312 43033312 5 43027662,43031154,43031790,43032080,43032797, 43027965,43031423,43031994,43032332,43033312, 0 FAM95B1 unk unk -1,-1,-1,-1,-1,', # nopep8
])


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