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.
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
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.
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 <[email protected]>
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.