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ConstructBuilder/ConstructBuilder.egg-info/PKG-INFO

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+Metadata-Version: 1.0
+Name: ConstructBuilder
+Version: 0.0.0
+Summary: UNKNOWN
+Home-page: UNKNOWN
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: UNKNOWN
+Description: UNKNOWN
+Platform: UNKNOWN

ConstructBuilder/ConstructBuilder.egg-info/SOURCES.txt

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+setup.py
+ConstructBuilder.egg-info/PKG-INFO
+ConstructBuilder.egg-info/SOURCES.txt
+ConstructBuilder.egg-info/dependency_links.txt
+ConstructBuilder.egg-info/top_level.txt

ConstructBuilder/ConstructBuilder.egg-info/dependency_links.txt

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+

ConstructBuilder/ConstructBuilder.egg-info/top_level.txt

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+

ConstructBuilder/builder.py

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+G = 'MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK'
+L2 = 'XXXXXXX'
+T = 'LEENLYFQS'
+L1 = 'GGSGGGSGGGSGGGS'
+H = 'HHHHHH'
+soluTag = {
+    'MBP': 'MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK',
+    'SUMO': 'MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV',
+    'Fh8': 'MPSVQEVEKLLHVLDRNGDGKVSAEELKAFADDSKCPLDSNKIKAFIKEHDKNKDGKLDLKELVSILSS',
+    'GST': 'MKLFYKPGACSLASHITLRESGKDFTLVSVDLMKKRLENGDDYFAVNPKGQVPALLLDDGTLLTEGVAIMQYLADSVPDRQLLAPVNSISRYKTIEWLNYIATELHKGFTPLFRPDTPEEYKPTVRAQLEKKLQYVNEALKDEHWICGQRFTIADAYLFTVLRWAYAVKLNLEGLEHIAAFMQRMAERPEVQDALSAEGLK',
+    'MBP': 'MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK',
+    'NusA': 'MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFRRWLVVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNISLDLGNNAEAVILREDMLPRENFRPGDRVRGVLYSVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVIEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTDDLQAKHQAEAHAAIDTFTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNALATIAQAQEESLGDNKPADDLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARNICWFGDEA',
+    'Thioredoxin': 'SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA',
+    'FLAG': 'DYKDDDDK',
+    'S-tag': 'KETAAAKFERQHMDS',
+    'CBP': 'KRRWKKNFIAVSAANRFKKISSSGAL',
+    'SUMO': 'MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV',
+    'STREPII': 'WSHPQFEK',
+    'BAP': 'GLNDIFEAQKIEWHE',
+    'NT11': 'VSEPHDYNYEK',
+    'Fh8': 'MPSVQEVEKLLHVLDRNGDGKVSAEELKAFADDSKCPLDSNKIKAFIKEHDKNKDGKLDLKELVSILSS',
+    'Tab2': 'VVSHFND',
+    'Z-basic': 'VDNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQPK',
+    'ProteinA': 'MKKKNIYSIRKLGVGIASVTLGTLLISGGVTPAANAAQHDEAQQNAFYQVLNMPNLNADQRNGFIQSLKDDPSQSANVLGEAQKLNDSQAPKADAQQNNFNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAPKADNNFNKEQQNAFYEILNMPNLNEEQRNGFIQSLKDDPSQSANLLSEAKKLNESQAPKADNKFNKEQQNAFYEILHLPNLNEEQRNGFIQSLKDDPSQSANLLAEAKKLNDAQAPKADNKFNKEQQNAFYEILHLPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNDAQAPKEEDNNKPGKEDNNKPGKEDNNKPGKEDNNKPGKEDNNKPGKEDGNKPGKEDNKKPGKEDGNKPGKEDNKKPGKEDGNKPGKEDGNKPGKEDGNGVHVVKPGDTVNDIAKANGADKIAADNKLADKNMIKPGQELVVDKKQPANHADANKAQALPETGEENPFIGTTVFGGLSLALGAALLEL',
+    'IMPACT': 'TNPGVSAWQVNTAYTAGQLVTYNGKTYKCLQPHTSLAGWEPSNVPALWQLQ',
+    'mysB': 'MTMYATLEEAIDAAREEFLADNPGIDAEDANVQQFNAQKYVLQDGDIMWQVEFFADEGEEGECLPMLSGEAAQSVFDGDYDEIEIRQEWQEENTLHEWDEGEFQLEPPLDTEEGRAAADEWDER',
+    'PolyR': 'RRRRR',
+    'c-myc': 'EQKLISEEDL',
+    'S': 'KETAAAKFERQHMDS',
+    'SBP-tag': 'MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP',
+    'Strep-tag': 'WRHPQFGG',
+    'Twin-Strep-tag': 'SAWSHPQFEKGGGSGGGSGGSAWSHPQFEK',
+    'HAT': 'KDHLIHNVHKEFHAHAHNK',
+    'BCCP': 'MDIRKIKKLIELVEESGISELEISEGEESVRISRAAPAASFPVMQQAYAAPMMQQPAQSNAAAPATVPSMEAPAAAEISGHIVRSPMVGTFYRTPSPDAKAFIEVGQKVNVDTLCIVEAMKMMNQIEADKSGTVKAILVESGQPVEFDEPLVVIE',
+    'HaloTag': 'SGSAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDKPDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPCGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISG'
+    }
+
+def run_N(P:str, gfp:bool, solu_tag:list)->dict:
+    const = {}
+    if gfp:
+        for f in solu_tag:
+            F = soluTag[f]
+            const[f"con_gfp_N_{f}"] = P+T+L1+F+L2+G+H
+        if not solu_tag:
+            const[f"con_gfp_N"] = P+T+L2+G+H
+    else:
+        for f in solu_tag:
+            F = soluTag[f]
+            const[f"con_N_{f}"] = P+T+L1+F+H
+        if not solu_tag:
+            const[f"con_N"] = P+T+H # TODO: verify this one
+    return const
+
+def run_C(P:str, gfp:bool, solu_tag:list)->dict:
+    const = {}
+    if gfp:
+        for f in solu_tag:
+            F = soluTag[f]
+            const[f"con_gfp_C_{f}"] = H+G+L2+F+L1+T+P
+        if not solu_tag:
+            const[f"con_gfp_C"] = H+G+L2+T+P
+    else:
+        for f in solu_tag:
+            F = soluTag[f]
+            const[f"con_C_{f}"] = H+F+L1+T+P
+        if not solu_tag:
+            const[f"con_C"] = H+T+P #TODO verify this
+    return const
+
+def build(P:str, solu_tag:list, GFP:bool, P_pos:str)->dict:
+    """
+    This function calculate constructs to Protera's LAB considering:
+        -orientation N to C terminal, or reverse
+        -With/withou GFP
+        -Fusion Proteins
+    
+    usage = build( amino_sequence, solutags, GFP:True/false, P_pos:"N+C","N","C")    
+    solutags availables:
+            'MBP', 'SUMO', 'Fh8', 'GST', 'NusA', 'Thioredoxin', 'FLAG', 'S-tag', 'CBP', 'STREPII', 'BAP', 'NT11', 'Tab2', 'Z-basic', 'ProteinA', 'IMPACT', 'mysB', 'PolyR', 'c-myc', 'S', 'SBP-tag', 'Strep-tag', 'Twin-Strep-tag', 'HAT', 'BCCP', 'HaloTag'
+    
+    """
+    if "all" in solu_tag:
+        solu_tag = list(soluTag.keys())
+    
+    d1 = {}
+    d2 = {}
+    
+    if  "C" in P_pos:
+        d2 = run_C(P, GFP, solu_tag)
+        
+    if "N" in P_pos:
+        d1 = run_N(P, GFP, solu_tag)
+        
+    return {**d1,**d2}

ConstructBuilder/setup.py

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+import setuptools
+setuptools.setup(name="ConstructBuilder")

construct.py

@@ -19,8 +19,8 @@ def LabFusion(name, file , uni_seq , orientation:str="NC", gfp:bool=False, sol_t
         dick[name] = build(uni_seq, sol_tag, gfp, orientation) 
     table = pd.DataFrame.from_dict(dick)
     
-    table.to_csv(f"/home/ubuntu/1TB_disk/constructos/gradio_projects/constructs_{name}.csv")
-    return table, f"/home/ubuntu/1TB_disk/constructos/gradio_projects/constructs_{name}.csv"
+    table.to_csv(f"./gradio_projects/constructs_{name}.csv")
+    return table, f"./gradio_projects/constructs_{name}.csv"
 
 
 int_align = gr.Interface(fn=LabFusion,