Skip to content

Commit

Permalink
Make example command lines readable
Browse files Browse the repository at this point in the history
  • Loading branch information
TomJKono committed Feb 10, 2016
1 parent a94d6c4 commit 2b4b94e
Showing 1 changed file with 9 additions and 3 deletions.
12 changes: 9 additions & 3 deletions SNPMeta_Manual.md
Original file line number Diff line number Diff line change
Expand Up @@ -312,6 +312,7 @@ below.
| `Disrupted STOP codon` | The mutation changes a STOP codon to a different codon. |
| `Premature STOP codon` | The mutation creates a STOP codon before the end of the annotated CDS. |

## Example Command Lines
We provide example data from the *Drosophila melanogaster* SNPs used to test
SNPMeta. These SNPs were constructed to have 60bp of sequence flanking each
query SNP. To annotate the provided SNPs against the best match in GenBank, type
Expand All @@ -322,15 +323,20 @@ query SNP. To annotate the provided SNPs against the best match in GenBank, type
annotations will be written to `stdout`. Supply the `-o` argument to have to
write to a file instead:

SNPMeta.py -f Example_SNPs.fasta -a '[email protected]' -l 60 \
SNPMeta.py -f Example_SNPs.fasta\
-a '[email protected]'\
-l 60\
-o SNPMeta_output.txt

To annotate the same SNPs against only *D. simulans*, it is possible to supply
only the `-t` argument, but it gives better results to also supply the `-q`
argument:

SNPMeta.py -f Example_SNPs.fasta -a '[email protected]' -l 60 \
-q 'Drosophila simulans' -t 'Drosophila simulans'
SNPMeta.py -f Example_SNPs.fasta\
-a '[email protected]'\
-l 60\
-q 'Drosophila simulans'\
-t 'Drosophila simulans'

`-q` is applied to the results returned by BLAST (it sends an Entrez query to
NCBI's servers), while `-t` acts on the GenBank records once they have been
Expand Down

0 comments on commit 2b4b94e

Please sign in to comment.