ropolomx / flumatch Goto Github PK

1. Specify path to blast files
2. Check if there are databases there
3. Error if they provided wrong path

Use os.osdir

Make few changes to libraries imported and syntax

Use os.makedir to create and os.access to check the directories exist

Design method to differentiate between H5 and H7 hi-path and low-path and classify strains accordingly. This can be part of the same script or part of a downstream application.

Very related to Issue #11 .

Two avenues can be taken here:

1. Use NCBI's Perl script and run a cron job as suggested here; or
2. Use the solution proposed by @dorbarker

for i in $(seq -w 0 99); do
    wget -q --continue --wait 10 --random-wait ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.${i}.tar.gz &&
    wget -q --continue --wait 10 --random-wait ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.${i}.tar.gz.md5 &&
    echo "Successfully retrieved nt.${i}.tar.gz" ||
    echo "nt.${i}.tar.gz failed or does not exist.";
done

Currently, the script returns a table with the annotated contig (query), target strain and other BLAST coverage information. It would be very nice to add metadata such as country by retrieving it from Genbank records. This could perhaps be done by feeding a list of accessions to a Genbank entrez search (in the style of this example. Alternatively, we could have a reference metadata table from FluDB, and then just cross-reference a list of accessions from the BLAST results to the information of that table

Currrently, the script stops (hangs up, really) at "Please rename your contigs or use --centre XXX to generate clean contig names" if FASTA headers are longer than 20 characters (prokka 1.11). If this happens, the program needs to exit.

Better yet: since this is a very common occurrence, a regex or a sed command could be integrated into the script so that this is taken care of during program run. Alternatively, sharing a sed command with the user to shorten the FASTA header could be a short-term solution.

Python or cat command ... or for loop from shell

It would be great to allow users to either start with raw reads and perform assembly with SPAdes or to start from assembled contigs. If we start with SPAdes assembly, then we should integrate annotation, BLAST search and report generation in the same script (the same way it is currently done if one starts with assembled contigs).

It would be good to parse and split the BLAST subject names so that each category would be displayed in a separate column/field

Current:

Desirable:

Currently the BLAST search uses the user-defined contig FASTA (i.e. args.contigs) as the query. However, using the strain/strain.ffn file generated by Prokka as the BLAST query is important because the FASTA headers of that file contain the annotation designated by Prokka.

Desired output:

Current output:

Alternatively, including both columns is also desirable: