Comments (2)
Hi Nate. Using mummer might be the easiest option. But, I guess the following python script might work as well:
from syri.pyxFiles.synsearchFunctions import samtocoords
import pandas as pd
al=samtocoords('PATH/TO/SAM/FILE')
al.to_csv('/PATH/TO/OUPUT/COORDS/FILE', sep='\t', index=False, header=False)
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Support for SAM/BAM is added with 95db3c6
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Related Issues (20)
- lack of the sequence information of variants HOT 2
- VCF4.2 HOT 2
- Duplications in previous version HOT 1
- Inversion breakpoint definition HOT 2
- What should be done if the genome has a different number of chromosomes? HOT 1
- IndexError: list index out of range HOT 3
- Inversion missed HOT 1
- can not output Syri.out HOT 4
- re-arragement between two Eukaryotic genomes HOT 1
- different names of sequences HOT 1
- Merge vcf from different sample HOT 1
- ERROR - Numerical chromosome id HOT 1
- Issue with alignment HOT 3
- Inversion disappears after running chroder HOT 3
- high fraction of inverted alignments HOT 2
- Installation error with conda create HOT 8
- KeyError thrown when running example with v1.6.3 HOT 6
- Import Error HOT 1
- the parameter --reg can not show Translocation HOT 1
- The question with "Unequal number of chromosomes in the genomes" error HOT 1
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