Command Line Options

You can see available command line options by typing python run_project -h:

harry@U36JC:~/code/discomark$ python run_project.py -h

DiscoMark v0.9

usage: run_project.py [-h] [-d DIR] [-i INPUT] [-r REFERENCE] [-s STEP]
                      [-a ANNOT] [-v] [--no-trim] [--no-primer-blast]

Discover phylogenetic markers from orthologous sequences.

optional arguments:
  -h, --help            show this help message and exit
  -d DIR, --dir DIR     working directory (where results will be stored)
  -i INPUT, --input INPUT
                        input folder for sample (at least two '-i' options
                        must be specified)
  -r REFERENCE, --reference REFERENCE
                        reference genome file (FASTA)
  -s STEP, --step STEP  start from step N
  -a ANNOT, --annot ANNOT
                        annotation file for input markers
  -v, --verbose         increase output verbosity
  --no-trim             skip alignment trimming step
  --no-primer-blast     skip online primer BLAST (use, when running without
                        internet connection

required parameters

The only required options are -i/--input (input location) and -d/--dir (output location).

input

Specify the -i/--input <folder> option for each taxon (e.g. individual or species) for which you have ortholog sequences. Make sure that <folder> specifies a valid path to the folder containing the FASTA files for the taxon.

If you are unsure if the path is valid, try typing ls <dirname>; if a list of FASTA files is displayed the path is correct:

harry@U36JC:~/code/discomark$ ls example/hamstr/Baetis/
411989.cds.fa  412085.cds.fa  412741.cds.fa  412840.cds.fa  413058.cds.fa
412045.cds.fa  412211.cds.fa  412814.cds.fa  412884.cds.fa  413088.cds.fa
412048.cds.fa  412698.cds.fa  412825.cds.fa  412985.cds.fa  413294.cds.fa

output location

The output folder (a/k/a "working directory") is specified by the -d/--dir option. All intermediate and final results will be placed in that directory.

optional parameters

Hint: While not required, specifying a reference genome can help a lot identifying intron/exon boundaries (in the case of RNA-seq or EST input data) or trimmed positions in the alignments.

reference

In case you have a reference genome for any of your input taxa, specify the corresponding FASTA file with the -r/--reference option, e.g. -r example/reference/Cloeon.fasta.

annotations

If you want to target specific sets of genes in your input data sets you can specify an annotation file with the -a/--annot option. If supplied, annotation terms will be included in the output to facilitate filtering for genes of interest.

Annotation files are simple TAB-separated files of the format "gene_id<TAB>annotation_term".

workflow control

repeating parts of a run

In case you want to try different configuration settings you can repeat parts of the pipeline by specifying the pipeline step to start from using the -s/--step option. In that case it is normally sufficient to specify the working directory and the step number, e.g.:

python run_project -d my_output/ -s 5

deactivating steps

Some steps of the pipeline might be unwanted (e.g. alignment trimming) or take a long time (e.g. online primer blast). You can use the following options to tell DiscoMark not to perform these steps:

--no-trim do not trim alignments (using TrimAl)

--no-primer-blast do not blast primers against NCBI database