From c61978a9c8eac041b378c53e7fc0095d2f36ed0c Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Tue, 28 May 2024 10:33:50 +0200
Subject: [PATCH] create a dict system -> model version
---
data/system-model-version.yaml | 147 ++++++++++++++++++
.../df-wiki-cli/df_wiki_cli/content/main.py | 5 +
2 files changed, 152 insertions(+)
create mode 100644 data/system-model-version.yaml
diff --git a/data/system-model-version.yaml b/data/system-model-version.yaml
new file mode 100644
index 00000000..cf4af5c5
--- /dev/null
+++ b/data/system-model-version.yaml
@@ -0,0 +1,147 @@
+AbiA: 1.2.2
+AbiB: 1.2.2
+AbiC: 1.2.2
+AbiD: 1.2.2
+AbiE: 1.2.2
+AbiG: 1.2.2
+AbiH: 1.2.2
+AbiI: 1.2.2
+AbiJ: 1.2.2
+AbiK: 1.2.2
+AbiL: 1.2.2
+AbiN: 1.2.2
+AbiO: 1.2.2
+AbiP2: 1.2.2
+AbiQ: 1.2.2
+AbiR: 1.2.2
+AbiT: 1.2.2
+AbiU: 1.2.2
+AbiV: 1.2.2
+AbiZ: 1.2.2
+Aditi: 1.2.2
+Avs: 1.2.3
+Azaca: 1.2.2
+BREX: 1.2.2
+Borvo: 1.2.2
+BstA: 1.2.2
+Bunzi: 1.2.2
+Butters_gp30_gp31: 1.2.3
+Butters_gp57r: 1.2.3
+CBASS: 1.2.2
+CapRel: 1.2.2
+Charlie_gp32: 1.2.3
+DISARM: 1.2.2
+DRT: 1.2.2
+DarTG: 1.2.2
+Dazbog: 1.2.2
+DdmDE: 1.2.4
+Detocs: 1.2.3
+Dnd: 1.2.2
+Dodola: 1.2.2
+Dpd: 1.2.2
+Druantia: 1.2.2
+Dsr: 1.2.2
+Eleos: 1.2.2
+FS_GIY_YIG: 1.2.3
+FS_HEPN_TM: 1.2.3
+FS_HP: 1.2.3
+FS_HP_SDH_sah: 1.2.3
+FS_HsdR_like: 1.2.3
+FS_Sma: 1.2.3
+GAPS1: 1.2.3
+GAPS2: 1.2.3
+GAPS4: 1.2.3
+GAPS6: 1.2.3
+Gabija: 1.2.2
+Gao_Ape: 1.2.2
+Gao_Her: 1.2.2
+Gao_Hhe: 1.2.2
+Gao_Iet: 1.2.2
+Gao_Mza: 1.2.2
+Gao_Ppl: 1.2.2
+Gao_Qat: 1.2.2
+Gao_RL: 1.2.2
+Gao_TerY: 1.2.2
+Gao_Tmn: 1.2.2
+Gao_Upx: 1.2.2
+GasderMIN: 1.2.2
+Hachiman: 1.2.2
+Hna: 1.2.3
+ISG15-like: 1.2.2
+JukAB: 1.2.3
+Kiwa: 1.2.2
+Lamassu-Fam: 1.2.3
+Lit: 1.2.2
+MADS: 1.2.3
+MMB_gp29_gp30: 1.2.3
+Menshen: 1.2.2
+Mok_Hok_Sok: 1.2.2
+Mokosh: 1.2.2
+MqsRAC: 1.2.2
+NLR: 1.2.2
+Nhi: 1.2.2
+NixI: 1.2.2
+Old_exonuclease: 1.2.2
+Olokun: 1.2.2
+PD-Lambda-1: 1.2.2
+PD-Lambda-2: 1.2.2
+PD-Lambda-3: 1.2.2
+PD-Lambda-4: 1.2.2
+PD-Lambda-5: 1.2.2
+PD-Lambda-6: 1.2.2
+PD-T4-1: 1.2.2
+PD-T4-10: 1.2.2
+PD-T4-2: 1.2.2
+PD-T4-3: 1.2.2
+PD-T4-4: 1.2.2
+PD-T4-5: 1.2.2
+PD-T4-6: 1.2.2
+PD-T4-7: 1.2.2
+PD-T4-8: 1.2.2
+PD-T4-9: 1.2.2
+PD-T7-1: 1.2.2
+PD-T7-2: 1.2.2
+PD-T7-3: 1.2.2
+PD-T7-4: 1.2.2
+PD-T7-5: 1.2.2
+Panchino_gp28: 1.2.3
+Paris: 1.2.3
+PfiAT: 1.2.2
+Phrann_gp29_gp30: 1.2.3
+Pif: 1.2.2
+PrrC: 1.2.2
+PsyrTA: 1.2.2
+Pycsar: 1.2.2
+RADAR: 1.2.2
+Retron: 1.2.2
+RexAB: 1.2.2
+RloC: 1.2.2
+RnlAB: 1.2.2
+RosmerTA: 1.2.2
+Rst_2TM_1TM_TIR: 1.2.2
+Rst_3HP: 1.2.2
+Rst_DUF4238: 1.2.2
+Rst_HelicaseDUF2290: 1.2.2
+Rst_Hydrolase-3Tm: 1.2.2
+Rst_RT-nitrilase-Tm: 1.2.2
+Rst_TIR-NLR: 1.2.2
+Rst_gop_beta_cll: 1.2.2
+SEFIR: 1.2.2
+SanaTA: 1.2.2
+Septu: 1.2.2
+Shango: 1.2.2
+Shedu: 1.2.2
+ShosTA: 1.2.2
+SoFIC: 1.2.2
+SpbK: 1.2.2
+SspBCDE: 1.2.2
+Stk2: 1.2.2
+Thoeris: 1.2.2
+Tiamat: 1.2.2
+Uzume: 1.2.2
+Viperin: 1.2.2
+Wadjet: 1.2.2
+Zorya: 1.2.2
+dCTPdeaminase: 1.2.2
+dGTPase: 1.2.2
+pAgo: 1.2.3
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 476e2514..918056ca 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -1,6 +1,7 @@
import typer
import sys
import json
+import yaml
import pandas as pd
import csv
import tempfile
@@ -281,6 +282,7 @@ def system_operon_structure(
model_dirs = list(download_model_release(releases))
systems = []
+ # system_model_version = {}
with open(structure) as tsvfile:
tsvreader = csv.DictReader(tsvfile, delimiter="\t")
for row in tsvreader:
@@ -298,6 +300,7 @@ def system_operon_structure(
):
system_genes_got.add(system_id)
def_path = find_model_definition(system, subsystem, list_paths)
+ # system_model_version[system] = def_path["version"]
in_exchangeables = False
current_gene = {}
exchangeables = []
@@ -356,6 +359,8 @@ def system_operon_structure(
# gene["alternatives"] = ",".join(gene["alternatives"])
gene["id"] = id
writer.writerow(gene)
+ # with open("./system-model-version.yaml", "w") as f_out:
+ # yaml.dump(system_model_version, f_out, default_flow_style=False)
def download_model_release(releases):
--
GitLab