Local Variants

LStructure was designed to analyze the results from diri_sampler. Its input:

• the support file (ending in reads-support.fas);
• the reference file (fasta reference used to run any of the shorah tools).

It does some postprocessing to improve the reliability and readability of variants:

• parses haplotypes with high posterior support (default: > 0.9) and minimum read count (default: 5 reads);
• corrects the single gaps frameshift inducing indels;
• resolves aminoacid indels to the closest possible correction;
• merges the identical haplotypes;
• eliminates haplotypes displaying SNVs removed looking at the strand bias;
• writes fasta files with frequencies, sorted;
• writes CSV files with the lists of single site mutations and their frequencies.

Default reference is HIV protease. Usage: LStructure.py -s support_file -r reference_file

Options:
    -h, --help            show this help message and exit
    -s SUPPORT, --support=SUPPORT
                support file
    -r REFERENCE, --reference=REFERENCE
                fasta file with reference

Requirements

3. Python3
4. Biopython
5. needle from EMBOSS software suite

Example

Add the `bin/` directory to your path and run the executable `localvar` as

[user@host amplicon_1]$ localvar -s your_window-support.fas -r HIV-HXB2.fasta
Reference is HIV-HXB2 from HIV
Total reads: 1017.959

[user@host amplicon_1]$ ls -1rht
...
mutations_DNA.csv
dna_seqs.fasta

The files listed above are the output of LocalVariants.