Date: 2019-08-16T23:07:24+08:00 A tool developed by Minghui Li Group and maintained by ZeFeng Zhu.
- 🔨 stands for [under construction]
Muta3DMaps is Python Package that retrieves, filtering and organizes data from various databases or tools via API to process the residue-level mapping between protein sequences and protein 3D structures.
- SIFTS
- UniProt
- wwPDB
- Interactome3D
- SWISS-MODEL Repository 🔨
- ModBase 🔨
- Collect data from SIFTS, UniProt, wwPDB(MMCIF), Interactome3D, SMR, ModBase
- Define representative structures(PDB or Model) of a uniprot(Canonical) with a score-based approach 🔨
- Map mutation from (transcript/UniProt) isoform to (Canonical UniProt/PDB/Model) or from PDB to UniProt Isoform.
-
Integrate multi-source data
-
Based on the flexible call to various open APIs without relying on the establishment of a personal database
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A transparent data handling process
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Good Data Accessibility and allow batch retrieve
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A bidirectional mapping
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Feedback on unmapped and untrusted results
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Add tags that help filtering results
>> Muta3DMaps("ENST00000541639", "S151C")
>> (("Q9BY66-3", "S151C"), ("2YQE", "A", 80, "S153C"))Correspondence Between Core Functions and
PYTHONFiles
ProcessUniProt.py- UniProt ID Mapping API
ProcessSIFTS.py- Map PDB to UniProt and vice versa
- Map PDB Mutation Site to UniProt and vice versa
RetrievePDB.py- Download PDB Files
ProcessMMCIF.py- Extract Info From mmCIF-format PDB Files
ProcessI3D.py- Retrieve and modify interactions info of Interactome3D
Representative.py🔨- Generate Representative Structure Dataset
ProcessSMR.py🔨- Retrieve and modify SWISS-MODEL Repository Info
ProcessModB.py🔨- Retrieve and modify ModBase Info
# Example
>> from Muta3DMaps.core.Mods import ProcessUniProt, RetrievePDB
>> help(RetrievePDB)Help on module Muta3DMaps.core.Mods.RetrievePDB in Muta3DMaps.core.Mods:
NAME
Muta3DMaps.core.Mods.RetrievePDB
DESCRIPTION
…
CLASSES
builtins.object
MPWrapper
RetrievePDB
class MPWrapper(builtins.object)
| MPWrapper(downloadPath, loggingPath, processes=3, maxSleep=3, ftpSite='RCSB', format='mmCIF')
|
| Multiprocessing wrapper for ``RetrievePDB``
|
| When there is a large number of PDB files to download, this class is helpful.
| But Need to be careful with the numbers of processes and the time of sleep.
…Usage: Muta3DMaps [OPTIONS] COMMAND [ARGS]...
Options:
--folder PATH The file folder of new files.
--help Show this message and exit.
Commands:
i3dmap
initmmcif
initsifts
inituniprot
initunpfasta
unp2pdb>Muta3DMaps --folder ./ inituniprot --help
Usage: Muta3DMaps inituniprot [OPTIONS]
Options:
--referenceFile PATH The reference file of IDs(with mutation Site) that
need to map via UniProt RESTful API.
--sep TEXT The seperator of referenceFile.
--idCol TEXT The column name of IDs in referenceFile.
--idType TEXT ID Abbreviation that stands for the type of ID.
--addUseCols TEXT Comma-separated list of the column names for
programmatic access to the UniProtKB search
results.
--siteCol TEXT The column name of aa site in referenceFile.
--geneCol TEXT The column name of gene info in referenceFile.
--procced / --no-procced Whether to procced after saving the site info.
--help Show this message and exit.>Muta3DMaps --folder ./ initunpfasta --help
Usage: Muta3DMaps initunpfasta [OPTIONS]
Options:
--fastaFolder PATH The file folder of UniProt FASTA Seq repository.
--unreviewed BOOLEAN Whethter to include FASTA Seq of unreviewed UniProt
Entry.
--isoform BOOLEAN Whethter to include isoform Seq.
--split BOOLEAN Whethter to split FASTA files.
--mode [wget|ftplib] Retrieve mode.
--fastaPath PATH The file path of downloaded fasta file.
--referenceFile PATH The file path of reference file that contains target
UniProt ID.
--sep TEXT The seperator of referenceFile.
--colName TEXT The column name of UniProt IDs in referenceFile.
--help Show this message and exit.>Muta3DMaps --folder ./ initsifts --help
Usage: Muta3DMaps initsifts [OPTIONS]
Options:
--test INTEGER Num of PDB IDs to test the program. Only for
test.
--unpFile PATH The file that comtains Target UniProt IDs.
--unpCol TEXT The column of UniProt IDs in unpFile.
--sep TEXT The seperator of unpFile.
--filtering <TEXT TEXT>... [filterColumn filterValue]: The filter of
unpFile. Keep the rows that have equal value in
filter column.
--useInitizedUnp BOOLEAN Whether to set the initialized result as the
unpFile.
--help Show this message and exit.>Muta3DMaps --folder ./ initmmcif --help
Usage: Muta3DMaps initmmcif [OPTIONS]
Options:
--pdbFolder PATH The file folder of PDB repository.
--pdbsFile PATH The file that comtains PDB IDs.
--pdbCol TEXT The column of PDB IDs in pdbsFile.
--sep TEXT The seperator of pdbsFile.
--help Show this message and exit.>Muta3DMaps --folder ./ unp2pdb --help
Usage: Muta3DMaps unp2pdb [OPTIONS]
Options:
--fastaFolder PATH The file folder of UniProt FASTA Seq repository.
--siteInfoFile PATH The file that comtains site info.
--help Show this message and exit.>Muta3DMaps --folder ./ i3dmap --help
Usage: Muta3DMaps i3dmap [OPTIONS]
Options:
--i3dPath PATH The downloaded file path of Interactome3D Meta file.
--help Show this message and exit.git clone https://github.com/NatureGeorge/Muta3DMaps
python setup.py install --record record.txtif you encounter this:
AttributeError: type object 'Callable' has no attribute '_abc_registry'when you use Muta3DMaps, you can either downgrad your Python to 3.6 or pip uninstall typing
See here for more information.
For the reason that biopython 1.75 has changed the way to set sub-matrix in Bio.Align and makes it becomes an unstable module to align sequences, 1.73, 1.74 versions are recommended.
FOR /F "delims=" %f in (record.txt) DO del "%f"pip install -i https://test.pypi.org/simple/ Muta3DMaps