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Commit c61978a9 authored by Remi  PLANEL's avatar Remi PLANEL
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create a dict system -> model version

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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
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):
......
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