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FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
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Include contig and position in SNP list #23

Open CarolineOhrman opened 4 years ago

CarolineOhrman commented 4 years ago

Copying issue from CanSNPer https://github.com/adrlar/CanSNPer/issues/28#issue-621253455

@standage commented

When I use the --snp_list option, I get a report like this.

SNP Derived Ancestral ft-asmbl.fna

B.1     T       C       T
B.2     T       G       T
B.3     T       C       T
B.4     A       T       T
B.5     T       C       T
B.6     T       C       C
B.7     G       A       A
B.8     T       G       G
B.9     C       T       T

I've been looking at the snp_lister function trying to figure out if there's any convenient way to include the contig ID and position aligned to that SNP.

#SNP    Derived Ancestral       ft-asmbl.fna     QuerySeq        QueryPosition
B.1     T       C       T       contig1 XXX
B.2     T       G       T       contig1 XXX
B.3     T       C       T       contig2 XXX
B.4     A       T       T       contig3 XXX
B.5     T       C       T       contig4 XXX

Would this be possible?