Generate mapping consensus data for SeqFindR

Generate PBS jobs given the inputs to SeqFindR_nesoni and submits the jobs. This is to complement SeqFindR (https://github.com/mscook/SeqFindR)

Assumes

• Have access to a cluster running PBSPro,
• Have Nesoni installed on the cluster and
• Have python >= 2.7

We use the database file (in multi-fasta format) as the reference.

The workflow is something like this:

$ nesoni make-reference myref ref-sequences.fa
$ ./SeqFindR_nesoni /path/to/reads/reads.dat /path/to/output/directory /path/to/mref/directory
649527[].paroo3
Warning : Job array will run for 0 days.

For each sample we then extract the consensus.fa file which we term the mapping consensus. This file is a multi-fasta file of the consensus base calls relative to the database sequences.

What does reads.dat look like?

For interleaved (default):

/path/to/rx.compression
/path/to/ry.compression
/path/to/rz.compression

For paired (-p):

/path/to/rx_1.compression
/path/to/rx_2.compression
/path/to/ry_1.compression
/path/to/ry_2.compression
/path/to/rz_1.compression
/path/to/rz_2.compression

Defining the read identifier

Without the -l flag the read ID's will become - rx, ry, and rz respectively.

For cases where you have reads that look like this:

/path/to/rubbish_rx_1_more_rubbish.compression
/path/to/rubbish_rx_2_more_rubbish.compression
/path/to/rubbish_ry_1_more_rubbish.compression
/path/to/rubbish_ry_2_more_rubbish.compression
/path/to/rubbish_rz_1_more_rubbish.compression
/path/to/rubbish_rz_1_more_rubbish.compression

you can use the -l flag (-l 2) in this case to get rx, ry, and rz.

Usage

Something like this:

$ ./SeqFindR_nesoni.py -h

usage: SeqFindR_nesoni.py [-h] [-v] [--version] [-p] [-i] [-d DELIM]
                          [-l IDENT_LOC] [-c CORES] [-m MEMORY]
                          reads_file output_base reference_dir

SeqFindR_nesoni v0.1 - Generate a nesoni run for SeqFindR

positional arguments:
  reads_file            Full path to a reads file
  output_base           Base location for nesoni output file to go
  reference_dir         Fullpath to the direcory created by nesoni make-
                        reference

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         verbose output
  --version             show program's version number and exit
  -p, --paired          Paired reads
  -i, --interleaved     Interleaved reads [Default = True]
  -d DELIM, --delim DELIM
                        Reads delimiter [Default = _ ]
  -l IDENT_LOC, --ident_loc IDENT_LOC
                        Reads identifier location [Default = 1 ]
  -c CORES, --cores CORES
                        CPU cores [Default = 4]
  -m MEMORY, --memory MEMORY
                        Memory [Default = 11]

Licence: ECL 2.0 by Mitchell Stanton-Cook <m.stantoncook@gmail.com>

Caveats

The (poor) alignment of reads at the start and the end of the database genes can result in N calls. This can result in downstream false negatives. We are currently working on solution to this.