mojaveazure/snp_utils

Extract SNP positions from BLAST XML and SAM formats

Hello World

I am Paul Hoffman, a senior bioinformatician with the Satija and Lappalainen Labs at the New York Genome Center. My work revolves around building software and for bioinformatic analyses, including an R package for analyzing single-cell data, along with several extension packages, and a pipeline for processing RNA-seq data. I work primarily in R and Python, but am always learning.

Social

Technologies Used

Basic Stats

Recent Activity

• Closed TileDB-Inc/tiledbsc#92
• Merged single-cell-data/TileDB-SOMA#990
• Opened single-cell-data/TileDB-SOMA#990
• Closed TileDB-Inc/TileDB-R#518
• Merged TileDB-Inc/TileDB-R#519
• Opened TileDB-Inc/TileDB-R#519
• Opened TileDB-Inc/TileDB-R#518
• Opened bnprks/BPCells#3
• Closed satijalab/seurat#6539
• Closed satijalab/seurat#6692

snp_utils's Issues

SNP_utils BLAST stop with errors

I'm trying to run snp_utils on Ubuntu 22.04 and python 3.10.6.
It generates the xml output file but later it stop with errors.
Below are the last lines on the shell. I cannot figure out what is happening.

No query found in GMI_ES02_c16875_166:8.60053e-64
hmm GMI_ES03_c17575_451:0.0
No reference allele for GMI_ES03_c17575_451:0.0, have you run Hsp.get_snp_position() yet?
hmm GMI_ES03_c17575_451:1.12148e-21
No query found in GMI_ES03_c17575_451:1.12148e-21
hmm GMI_ES03_c17575_451:3.55129e-111
No query found in GMI_ES03_c17575_451:3.55129e-111
hmm GMI_ES03_c17575_451:5.21775e-20
No query found in GMI_ES03_c17575_451:5.21775e-20
hmm GMI_ES03_c17575_451:5.21775e-20
No query found in GMI_ES03_c17575_451:5.21775e-20
hmm GMI_ES03_c17370_63:1.92383e-137
Traceback (most recent call last):
File "/home/davide/Programs/SNP_Utils-master/snp_utils.py", line 285, in
main()
File "/home/davide/Programs/SNP_Utils-master/snp_utils.py", line 262, in main
snp_list, no_snps, ref_gen, bconf = blast_based(args, lookup_dict)
File "/home/davide/Programs/SNP_Utils-master/snp_utils.py", line 103, in blast_based
hsp.add_snp(lookup=lookup)
File "/home/davide/.local/lib/python3.10/site-packages/overload.py", line 181, in f
return callable(*usable_args, **_kw)
File "/home/davide/Programs/SNP_Utils-master/Objects/blast.py", line 267, in add_snp
self.add_snp(this_snp=snp.SNP(lookup=lookup, hsp=self))
File "/home/davide/.local/lib/python3.10/site-packages/overload.py", line 181, in f
return callable(*usable_args, **_kw)
File "/home/davide/Programs/SNP_Utils-master/Objects/snp.py", line 103, in init
self._position = hsp.get_snp_position(lookup=lookup)
File "/home/davide/.local/lib/python3.10/site-packages/overload.py", line 181, in f
return callable(*usable_args, **_kw)
File "/home/davide/Programs/SNP_Utils-master/Objects/blast.py", line 233, in get_snp_position
return self.get_snp_position(query_snp=lookup.get_code(), expected=adj)
File "/home/davide/.local/lib/python3.10/site-packages/overload.py", line 181, in f
return callable(*usable_args, **_kw)
File "/home/davide/Programs/SNP_Utils-master/Objects/blast.py", line 198, in get_snp_position
raise NoSNPError("Cannot find the SNP in " + self) # Error out to avoid infinite loops
TypeError: can only concatenate str (not "Hsp") to str

Some of the physical positions are wrong due to the gap in the reference

There is a bug, which can not take care of the gap in the reference. So some of the physical positions are wrong.
The examples I found are here: /panfs/roc/scratch/llei/wrong_position_SNPuti