From 0117eb69820903ead65c9b19da4624b1550d639b Mon Sep 17 00:00:00 2001 From: "Laura Luebbert, Ph.D." <56094636+lauraluebbert@users.noreply.github.com> Date: Wed, 9 Oct 2024 04:24:20 +0200 Subject: [PATCH] Split complex Python example for easier reading --- docs/src/es/mutate.md | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/docs/src/es/mutate.md b/docs/src/es/mutate.md index 088682eb..3b93056c 100644 --- a/docs/src/es/mutate.md +++ b/docs/src/es/mutate.md @@ -194,9 +194,25 @@ gget mutate \ ``` ```python # Python -gget.mutate(sequences="genome_reference.fa", mutations="mutations_input.csv", out="mut_fasta.fa", k=4, seq_id_column="Chromosome", mut_column="Mutation", gtf="genome_annotation.gtf", gtf_transcript_id_column="Ensembl_Transcript_ID", optimize_flanking_regions=True, update_df=True, update_df_out="mutations_updated.csv", store_full_sequences=True, translate=True, translate_start="Translate_Start", translate_end="Translate_End") -``` -→ Toma el archivo 'mutations_input.csv' que contiene: +gget.mutate( + sequences="genome_reference.fa", + mutations="mutations_input.csv", + out="mut_fasta.fa", + k=4, + seq_id_column="Chromosome", + mut_column="Mutation", + gtf="genome_annotation.gtf", + gtf_transcript_id_column="Ensembl_Transcript_ID", + optimize_flanking_regions=True, + update_df=True, + update_df_out="mutations_updated.csv", + store_full_sequences=True, + translate=True, + translate_start="Translate_Start", + translate_end="Translate_End" +) +``` +→ Toma un genoma fasta ('genome_reference.fa') y un archivo gtf ('genome_annotation.gtf') (estos se pueden descargar usando [`gget ref`](ref.md)), así como un archivo 'mutations_input.csv' que contiene: ``` | Chromosome | Mutation | Ensembl_Transcript_ID | Translate_Start | Translate_End | |------------|-------------------|------------------------|-----------------|---------------|