Package checkm
source code
Checkm
======
Implementation of the Checkm specifications at http://www.cdlib.org/inside/diglib/checkm/checkmspec.html
NOTICE
======
The Checkm specification on which this implementation is based is (c) 2009 UC Regents.
This implementation is released under the Apache licence
checkm - cli script
===================
Usage: checkm [options] command filenames
Commands:
checkm write [checkm filename (default:checkm.txt) [filepath (default='.')]]
- writes a checkm manifest file to disc for the files in the given filepath.
Use -r to include all files under a given path in a single manifest.
checkm print [filepath (default='.')]
- As for 'write', but will print the manifest to the screen.
checkm multi [checkm filename (default:checkm.txt) [filepath (default='.')]]
- writes a checkm manifest file to disc for the files in the given filepath, recursively creating a manifest file within each subdirectory and using the '@' designation in the parent checkm files above it.
checkm check [checkm filename (default:checkm.txt)]
- checks the given checkm manifest against the files on disc.
Use -m to recursively scan through any multilevel checkm files it finds in this manifest as well.
checkm remove_multi [checkm filename (default:checkm.txt)]
- scans through the checkm file, recursively gathering a list of all included checkm manifests, returning the list of files.
Use the option '-f' or '--force' to cause the tool to try to delete these checkm files.
checkm - tool to create, check and remove checkm manifests
Options:
-h, --help show this help message and exit
-a ALG, --algorithm=ALG
Algorithm to use to hash files
-v, --verbose Log information to stdin as it goes
-r, --recursive Recursively scan through child directories
-m, --multi Recursively scan through @Checkm manifests as well
-f, --force Required when recursively deleting multilevel checkm
files - if not added, the command will lsit the files
it would've deleted
API documentation - TODO!
|
COLUMNS = { 0: ' SourceFileOrURL ' , 1: ' Alg ' , 2: ' Digest ' , 3: ' Le ...
|
|
SF_APPEND = 262144
|
|
SF_ARCHIVED = 65536
|
|
SF_IMMUTABLE = 131072
|
|
SF_NOUNLINK = 1048576
|
|
SF_SNAPSHOT = 2097152
|
|
ST_ATIME = 7
|
|
ST_CTIME = 9
|
|
ST_DEV = 2
|
|
ST_GID = 5
|
|
ST_INO = 1
|
|
ST_MODE = 0
|
|
ST_MTIME = 8
|
|
ST_NLINK = 3
|
|
ST_SIZE = 6
|
|
ST_UID = 4
|
|
S_ENFMT = 1024
|
|
S_IEXEC = 64
|
|
S_IFBLK = 24576
|
|
S_IFCHR = 8192
|
|
S_IFDIR = 16384
|
|
S_IFIFO = 4096
|
|
S_IFLNK = 40960
|
|
S_IFREG = 32768
|
|
S_IFSOCK = 49152
|
|
S_IREAD = 256
|
|
S_IRGRP = 32
|
|
S_IROTH = 4
|
|
S_IRUSR = 256
|
|
S_IRWXG = 56
|
|
S_IRWXO = 7
|
|
S_IRWXU = 448
|
|
S_ISGID = 1024
|
|
S_ISUID = 2048
|
|
S_ISVTX = 512
|
|
S_IWGRP = 16
|
|
S_IWOTH = 2
|
|
S_IWRITE = 128
|
|
S_IWUSR = 128
|
|
S_IXGRP = 8
|
|
S_IXOTH = 1
|
|
S_IXUSR = 64
|
|
UF_APPEND = 4
|
|
UF_IMMUTABLE = 2
|
|
UF_NODUMP = 1
|
|
UF_NOUNLINK = 16
|
|
UF_OPAQUE = 8
|
|
__package__ = ' checkm '
|
|
logger = logging.getLogger('checkm')
|
COLUMNS
- Value:
{ 0: ' SourceFileOrURL ' ,
1: ' Alg ' ,
2: ' Digest ' ,
3: ' Length ' ,
4: ' ModTime ' ,
5: ' TargetFileOrURL ' }
|
|