From 8901c156f5035289e6615ed314027659244ae4e1 Mon Sep 17 00:00:00 2001 From: Carlo Fisicaro <66260709+CFisicaro@users.noreply.github.com> Date: Thu, 9 Dec 2021 14:29:14 +0100 Subject: [PATCH 1/2] docs(README): update --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6e8873a..85be21d 100644 --- a/README.md +++ b/README.md @@ -161,7 +161,7 @@ Where: - `` defines the FASTA file containing the proteins for which you want to compute the intrinsic disorder - `` defines the path where you want to save the residue level representations -- `--msa` runs the procedure to get `esm-msa` representations (**optional**) +- `--msa` runs the [MSA procedure](MSA setting (optional)) to get `esm-msa` representations. We suggest you take a look to the [MSA inference](scripts/adopt_msa_inference.sh) script as a quick example (**optional**) - `-h` shows help message and exit A subdirectory containing the residue level representation extracted from each pre-trained model available will be created under both the `residue_level_representation_dir`. @@ -225,7 +225,7 @@ Where: - `` defines the path where we saved the residue level representations of the proteins in the *training set* - `` defines the path where we saved the residue level representations of the proteins in the *test set* - `--train_strategy` defines the **training strategies** defined above -- `--msa` runs the procedure to get trained models fed with the `esm-msa` representations (**optional**) +- `--msa` runs the [MSA procedure](MSA setting (optional)) to get trained models fed with the `esm-msa` representations. We suggest you take a look to the [MSA training](scripts/adopt_chezod_msa_training.sh) script as a quick example (**optional**) - `-h` shows help message and exit ## Citations From 62ef913ddbbe20b853b7d1763190dd97005a7098 Mon Sep 17 00:00:00 2001 From: Carlo Fisicaro <66260709+CFisicaro@users.noreply.github.com> Date: Thu, 9 Dec 2021 14:33:20 +0100 Subject: [PATCH 2/2] docs(README): update --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 85be21d..2de99b9 100644 --- a/README.md +++ b/README.md @@ -161,7 +161,7 @@ Where: - `` defines the FASTA file containing the proteins for which you want to compute the intrinsic disorder - `` defines the path where you want to save the residue level representations -- `--msa` runs the [MSA procedure](MSA setting (optional)) to get `esm-msa` representations. We suggest you take a look to the [MSA inference](scripts/adopt_msa_inference.sh) script as a quick example (**optional**) +- `--msa` runs the [MSA procedure](#msa-setting-optional) to get `esm-msa` representations. We suggest you take a look to the [MSA inference](scripts/adopt_msa_inference.sh) script as a quick example (**optional**) - `-h` shows help message and exit A subdirectory containing the residue level representation extracted from each pre-trained model available will be created under both the `residue_level_representation_dir`. @@ -225,7 +225,7 @@ Where: - `` defines the path where we saved the residue level representations of the proteins in the *training set* - `` defines the path where we saved the residue level representations of the proteins in the *test set* - `--train_strategy` defines the **training strategies** defined above -- `--msa` runs the [MSA procedure](MSA setting (optional)) to get trained models fed with the `esm-msa` representations. We suggest you take a look to the [MSA training](scripts/adopt_chezod_msa_training.sh) script as a quick example (**optional**) +- `--msa` runs the [MSA procedure](msa-setting-optional) to get trained models fed with the `esm-msa` representations. We suggest you take a look to the [MSA training](scripts/adopt_chezod_msa_training.sh) script as a quick example (**optional**) - `-h` shows help message and exit ## Citations