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- builtins.object
-
- BIRCHSettings
- BLASTDBList
- FileMetaData
- Parameters
class BIRCHSettings(builtins.object) |
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Data and methods for the BIRCH Settings file.
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Methods defined here:
- ReadBIRCHSettings(self, FN)
- Read current values of BIRCHvariables from BIRCH.settings.
- WriteBIRCHSettings(self, SFN)
- Write current values of BIRCHvariables to BL.properties.<platform> file.
- WriteBIRCHenvBourne(self, P)
- Write bash code for setting BIRCHvariables to birch_settings_Bourne.source.
Used for Bourne type shells eg. bash, sh
- WriteBIRCHenvCsh(self, P)
- Write csh code for setting BIRCHvariables to birch_settings_csh.source.
Used for C type shells eg. csh, tcsh
- __init__(self, P)
- Initializes arguments:
dict = {}
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class BLASTDBList(builtins.object) |
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Data and methods for the BLAST databases.
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Methods defined here:
- AddFiles(self, P, DBNAMES_INSTALLED, DBNAMES_ALL, LOGFILE)
- Cycle through the names of databases in the order given in UpdateList.
- CheckBLASTDB(self, BLASTDB, DBNAMES_ALL)
- Get a list of databases found in the BLASTDB directory.
There are potentially a lot of ways this might be done,
and no obvious best choice. Here, we just look to make sure
that each database name is found, regardless of how many
files share that name eg. nt includes files with names like
nt.01.*
- CheckFTPsite(self, FTPSITE, DBNAMES_ALL)
- Get a list of database files found at the remote FTP site.
- CreateBLMenu(self, P, DBNAMES, Directory, TNAME)
- Create a BioLegato .blmenu file from a template file
- CreateFastaNamefiles(self, BIRCHDIR, BLASTDB, DBNAMES_INSTALLED)
- Create .nam files so that FASTA can find BLAST
databases.
- FindNewFiles(self, DBLIST)
- Return a list of database files .tar.gz files that are newer on the server than
those in the local directory. In practice, this means that
if the local *.tar.gz.md5 file is older than the *.tar.gz.md5
file on the remote site, we download the newer *.tar.gz files from the
remote site.
- ReadBLASTDBList(self, FN, DBNAMES_ALL)
- Read list of BLAST databases, descriptions and install status (0,1).
- Revise(self, P, DBNAMES_ALL)
- Revise local database metadata, BioLegato menus and FASTA .nam files
- UpdateFiles(self, P, DBNAMES_INSTALLED, DBNAMES_ALL, LOGFILE)
- Cycle through the names of databases in the order given in UpdateList.
If the name is in the list to be updated, first delete the files for that
name to create some space. Next download and install
the new files. When all files have been downloaded, send an email to the
BIRCH administrator.
- WriteBLASTDBList(self, DBNAMES_ALL)
- Write list of BLAST databases, descriptions and install status (0,1).
- WriteFTPReport(self, BLASTDB, FTPSITE, DBNAMES_ALL)
- Write a spreadsheet-ready report with statistics on the remote NCBI databases.
The report is a tab-separated value file written to $BLASTDB/ftpstats.tsv.
- WriteLocalReport(self, BLASTDB, DBNAMES_INSTALLED)
- Write a spreadsheet-ready report with statistics on the local copy of the NCBI databases.
The report is a tab-separated value file written to $BLASTDB/localstats.tsv.
- __init__(self, P, DBNAMES_ALL)
- Initializes local BLASTDB list and sets DBNAMES_ALL
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class FileMetaData(builtins.object) |
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Holds metadata for a file.
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Methods defined here:
- __init__(self)
- Initializes arguments:
Name = ""
Size = 0
MDate = datetime.time()
- getFTPMetaData(self, line, UseMLSD)
- Parse metadata for a file on a remote FTP site.
- getLocalMetaData(self, FN)
- Retrieve metadata for a local file.
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class Parameters(builtins.object) |
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Wrapper class for command line parameters
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Methods defined here:
- __init__(self)
- Initializes arguments:
SHOWALL = False
CONFIGURE = False
BIRCHDIR = ""
BLASTDB = ""
REPORTLOCAL = False
REPORTFTP = False
ADD = False
DELETE = False
UPDATE = False
FTPSITE = ""
DBLIST = []
SFN= ""
Then calls read_args() to fill in their values from command line
- read_args(self)
- Read command line arguments into a Parameter object
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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