Commit adba0aac authored by Sam Nooij's avatar Sam Nooij
Browse files

Remove gene info table

This table is not used currently
parent b470b39d
......@@ -35,11 +35,7 @@ It is assumed that these inputfiles are stored under `data/raw/`, as `all_taxCla
Species of interest need to be given by the user, as name. E.g. '_Escherichia coli_' is a valid name. Genus names such as '_Clostridium_' work as well.
These should be entered into the pipeline configuration file: `config/config.yaml`.
Sequences to screen for may be any sequence as fasta file. This file should be listed in the `config/config.yaml` file. Additionally, a table with alternative names for the sequences may be entered. This is useful when screening for genes from GenBank, e.g. when you are looking for the _colibactin A_ gene (clbA) and your reference fasta has the label "lcl|CP025328.1_cds_AUG64981.1_5 [gene=clbA] [locus_tag=CXG97_11595] [protein=colibactin biosynthesis phosphopantetheinyl transferase ClbA] [protein_id=AUG64981.1] [location=2190549..2191283] [gbkey=CDS]", and you want to list just "clbA". A tab-separated table like below can be used to insert better readable names in figures.
| Long_name | Long_ID | Accession | Gene |
| --------- | ------- | --------- | ---- |
| lcl\|CP025328.1_cds_AUG64981.1_5 [gene=clbA] [locus_tag=CXG97_11595] [protein=colibactin biosynthesis phosphopantetheinyl transferase ClbA] [protein_id=AUG64981.1] [location=2190549..2191283] [gbkey=CDS] | lcl\|CP025328.1_cds_AUG64981.1_5 | AUG64981 | clbA |
Sequences to screen for may be any sequence as fasta file. This directory with fasta files should be listed in the `config/config.yaml` file, next to `reference_directory: `.
When these files are provided to the pipeline, it will try to:
......@@ -107,7 +103,6 @@ conda env create -f envs/snakemake.yaml
The 'snakemake' environment includes `snakemake` and `pyyaml`, which are needed to run all the main commands listed below.
### 3. Prepare data
#### Import from Jovian
......@@ -268,7 +263,7 @@ snakemake -p --use-conda --latency-wait 60 --jobs 10 \
```
On a SLURM-based system. (Make sure to create the `log/SLURM` folder,
or change it to an existing folder name before running this.)
or change the command to an existing folder name before running this.)
_Additionally, for me Snakemake did not seem to communicate well with SLURM._
_Snakemake could not get the status for each job, which it told as errors on the Terminal._
......
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