02-11-2012
finding, copying, assembling
Hi everybody,
I've been running some analyses, the results of which have been stored in a sequential manner with a directory structure like step0, step1, step2, ... for iterations 0-2, for example. Each iteration contains several nested folders, with three pieces of information I need. I need to do the following:
(1) Find within each iteration directory, and extract sequentially to a new file, the number following the text, "final GAMMA-based Likelihood:" The numbers need to be in a list whose order preserves the original order (iteration 0, 1, 2, ...).
(2) Find, copy, and concatenate into a single file the contents of the file "RAxML_bestTree.default." As for (1), the order should preserve the iteration order.
(3) Copy the file "input.phy" to a new directory called alignments, preserving the order of the iterations, and renaming the file to correspond to the iteration number, e.g. input.phy.0, inpout.phy.1, etc.
I anticipate this will require some grep and for loops, but I am very much unsure of how to proceed.
Thanks!
~John
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LEARN ABOUT DEBIAN
smp_rep_route_info
SMP_REP_ROUTE_INFO(8) SMP_UTILS SMP_REP_ROUTE_INFO(8)
NAME
smp_rep_route_info - invoke REPORT ROUTE INFORMATION SMP function
SYNOPSIS
smp_rep_route_info [--help] [--hex] [--index=IN] [--interface=PARAMS] [--multiple] [--num=NUM] [--phy=ID] [--raw] [--sa=SAS_ADDR] [--ver-
bose] [--version] [--zero] SMP_DEVICE[,N]
DESCRIPTION
Sends a SAS Management Protocol (SMP) REPORT ROUTE INFORMATION function request to a SMP target. The SMP target is identified by the
SMP_DEVICE and the SAS_ADDR. Depending on the interface, the SAS_ADDR may be deduced from the SMP_DEVICE. The mpt interface uses SMP_DEVICE
to identify a HBA (an SMP initiator) and needs the additional ,N to differentiate between HBAs if there are multiple present.
There are two expander route table types: phy-based and expander-based. The expander-based route table was introduced in SAS-2 and super-
sedes the phy-based route tables. The REPORT ROUTE INFORMATION function is associated with a phy-based route table. The CONFIGURE ROUTE
INFORMATION function is provided to manually set up a phy-based route table.
Each phy in a SAS expander that has an associated routing attribute of "table" has a router table. The number of rows (or entries) in each
router table is given by the "expander route indexes" field in the response of the REPORT GENERAL function.
When the --multiple option is given, the REPORT ROUTE INFORMATION function is called multiple times. The index value increments on each
iteration, starting from --index=IN (default 0). If --num=NUM is given and NUM is greater than zero then that is the maximum number of
iterations performed. If --num=NUM is not given (or NUM is zero) then iterations continue until there are 4 adjacent disabled route entries
(or some error is detected).
OPTIONS
Mandatory arguments to long options are mandatory for short options as well.
-h, --help
output the usage message then exit.
-H, --hex
output the response (less the CRC field) in hexadecimal.
-i, --index=IN
expander route index. IN is a value between 0 and 65535. Default is 0. More precisely the maximum index value is
(expander_route_indexes - 1).
-I, --interface=PARAMS
interface specific parameters. In this case "interface" refers to the path through the operating system to the SMP initiator. See
the smp_utils man page for more information.
-m, --multiple
call the REPORT ROUTE INFORMATION function multiple times, starting at --index=IN, incrementing the index value on each iteration
for a maximum of --num=NUM iterations. For each enabled route table entry, one line is output. If --num=NUM is not given (or NUM is
zero) then iterations continue until 4 adjacent disabled entries are found (or some error occurs).
-n, --num=NUM
used with --multiple option to specify the maximum number of iterations.
-p, --phy=ID
phy identifier. ID is a value between 0 and 254. Default is 0.
-r, --raw
send the response (less the CRC field) to stdout in binary. All error messages are sent to stderr.
-s, --sa=SAS_ADDR
specifies the SAS address of the SMP target device. Typically this is an expander. This option may not be needed if the SMP_DEVICE
has the target's SAS address within it. The SAS_ADDR is in decimal but most SAS addresses are shown in hexadecimal. To give a number
in hexadecimal either prefix it with '0x' or put a trailing 'h' on it.
-v, --verbose
increase the verbosity of the output. Can be used multiple times.
-V, --version
print the version string and then exit.
-z, --zero
zero the Allocated Response Length field in the request. This option also zeros the Request Length field in the request. This is
required for strict SAS-1.1 compliance. However this option should not be given in SAS-2 and later; if it is given an abridged
response may result.
CONFORMING TO
The SMP REPORT ROUTE INFORMATION function was introduced in SAS-1 . The "Expander change count" field was added in SAS-2 .
AUTHORS
Written by Douglas Gilbert.
REPORTING BUGS
Report bugs to <dgilbert at interlog dot com>.
COPYRIGHT
Copyright (C) 2006-2011 Douglas Gilbert
This software is distributed under a FreeBSD license. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR-
POSE.
SEE ALSO
smp_utils, smp_rep_general(smp_utils)
smp_utils-0.96 May 2011 SMP_REP_ROUTE_INFO(8)