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The equal sign is not escaped in output #171

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ericblanc20 opened this issue Feb 22, 2024 · 0 comments · May be fixed by #172
Open

The equal sign is not escaped in output #171

ericblanc20 opened this issue Feb 22, 2024 · 0 comments · May be fixed by #172

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@ericblanc20
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  • vcfpy version: 0.13.6
  • Python version: 3.10.13
  • Operating System: Rocky Linux 8.7 (Green Obsidian), Linux 4.18.0-348.2.1.el8_5.x86_64

Description

Escaping the equal sign = in INFO fields is lost on writing.

What I Did

$ grep 86112567 input.vcf
chr1	86112567	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=167,122|3,3;DP=297;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=163,180;MMQ=60,60;MPOS=17;NALOD=1.71;NLOD=15.05;POPAF=6;ROQ=33;TLOD=6.38;CSQ=T|splice_region_variant&synonymous_variant|LOW|COL24A1|ENSG00000171502|Transcript|ENST00000370571|protein_coding|5/60||ENST00000370571.7:c.1599G>A|ENSP00000359603.2:p.Lys533%3D|1975|1599|533|K|aaG/aaA|||-1||SNV|HGNC|HGNC:20821|YES|NM_152890.7|1|P1|CCDS41353.1|ENSP00000359603|Q17RW2.126||UPI000013E81F|Q17RW2-1||Ensembl||C|C|||||Low_complexity_(Seg):seg&PANTHER:PTHR24023&PANTHER:PTHR24023:SF977&Pfam:PF01391||||||||||||||||||||||||||||||;ACGTNacgtnPLUS=0,67,0,3,0,0,5,0,1,0;ACGTNacgtnMINUS=0,56,0,0,0,0,8,0,0,0	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:88,0:0.019:88:22,0:27,0:50,0:47,41,0,0	0/1:201,6:0.035:207:68,4:63,0:135,4:120,81,3,3
$ python
>>> import vcfpy
>>> reader = vcfpy.Reader.from_path("input.vcf")
>>> writer = vcfpy.Writer.from_path("output.vcf", reader.header)
>>> for record in reader:
...     writer.write_record(record)
... 
>>> 
$ grep 86112567 output.vcf
chr1	86112567	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=167%2C122|3%2C3;DP=297;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=163,180;MMQ=60,60;MPOS=17;NALOD=1.71;NLOD=15.05;POPAF=6.0;ROQ=33.0;TLOD=6.38;CSQ=T|splice_region_variant&synonymous_variant|LOW|COL24A1|ENSG00000171502|Transcript|ENST00000370571|protein_coding|5/60||ENST00000370571.7:c.1599G>A|ENSP00000359603.2:p.Lys533=|1975|1599|533|K|aaG/aaA|||-1||SNV|HGNC|HGNC:20821|YES|NM_152890.7|1|P1|CCDS41353.1|ENSP00000359603|Q17RW2.126||UPI000013E81F|Q17RW2-1||Ensembl||C|C|||||Low_complexity_(Seg):seg&PANTHER:PTHR24023&PANTHER:PTHR24023:SF977&Pfam:PF01391||||||||||||||||||||||||||||||;ACGTNacgtnPLUS=0,67,0,3,0,0,5,0,1,0;ACGTNacgtnMINUS=0,56,0,0,0,0,8,0,0,0	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:88,0:0.019:88:22,0:27,0:50,0:47,41,0,0	0/1:201,6:0.035:207:68,4:63,0:135,4:120,81,3,3

The escaped equal sign in the input file (...p.Lys%3D|...) is lost in the output file (...p.Lys533=|...).

(The commas , that are present in the input file are correctly escaped on output)
@ericblanc20 ericblanc20 linked a pull request Feb 22, 2024 that will close this issue
fix: escaped equal sign in INFO fields #172
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fix: escaped equal sign in INFO fields bihealth/vcfpy
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@ericblanc20