Analysis of protein coding exons in single molecule assemblies
- splign (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi?textpage=downloads)
- Python 3.5
git clone https://github.com/WatsonLab/sm_assemblies.git cd sm_assemblies
/bin/bash scripts/download.sh gunzip *.fasta.gz mkdir genomes mv *.fasta genomes
Perl script alnparse.pl can be used to summarise the splign output.
The way the pipeline stores splign results is in a "one query, one subject" file i.e. "ENST00000052569.10.OCVW01001666.1.aln" - this would be all of the splign hits from ENST00000052569.10 (query) against OCVW01001666.1 (subject).
To summarise the best hit from a single alignment file, run the script like this:
perl scripts/alnparse.pl ENST00000052569.10.OCVW01001666.1.aln
However, often we want to consider the hits against multiple subjects in order to find the best hit. In this case, we run it like this:
perl scripts/alnparse.pl <(cat ENST00000052569.10.*.aln)
This will find the best hit from alignments of ENST00000052569.10 against all subjects it has been aligned against.
The output is tab-delimited:
- query name
- hit name
- query start
- length of alignment
- number of mismatch events
- number of bases in mismatch events
- number of insertion events
- number of bases in insertion events
- number of deletion events
- number of bases in deletion events
- protein sequence of aligned bases