Hi everyone,
I need to know how to remove a chunk of codes from a file
for instance i have couple of lines which are commented out of the file and i need to remove that block. here is the example
--#------------------------------------------------------------------
--# File name= ... (5 Replies)
Hi,
I do have a TAB delimted text file with the following format.
1 (- identifier of each group. this text is not present in the file only number)
1 3 4 65 56 WERTF
2 3 4 56 56 GHTYHU
3 3 5 64 23 VMFKLG
2
1 3 4 65 56 DGTEYDH
2 3 4 56 56 FJJJCKC
3 3 5 64 23 FNNNCHD
3
1 3 4 65 56 JDHJDH... (9 Replies)
Hi all,
I have the following script, but are not too sure about the syntax to complete the script.
In essence, the script must connect to a SFTP server at a client site with username and password located in a file on my server.
Then change to the appropriate directory.
Pull the data to the... (1 Reply)
Hi All
I wanted to know how to effectively delete some columns in a large tab delimited file.
I have a file that contains 5 columns and almost 100,000 rows
3456 f g t t
3456 g h
456 f h
4567 f g h z
345 f g
567 h j k lThis is a very large data file and tab delimited.
I need... (2 Replies)
Hi All,
I need some help to effectively parse out a subset of results from a big results file.
Below is an example of the text file. Each block that I need to parse starts with "Output of GENE for sequence file 100.fasta" (next block starts with another number). I have given the portion of... (8 Replies)
Hi Gurus,
I need some help in extracting some of these information and massage it into the desired output as shown below.
I need to extract the last row with the header in below sample which is usually the most recent date, for example:
2012-06-01 142356 mb 519 -219406 mb 1 ... (9 Replies)
Hi ,
I am getting file name like
ABC_DATA_CUSTIOMERS_20120617.dat
ABC_DATA_PRODUCTS_20120617.dat
Need to convert
CUSTIOMERS.dat
PRODUCTS.dat
Help me how to do this. (7 Replies)
Need to sort a portion of a file in a Alphabetical Order.
Example : The user adam is not sorted and the user should get sorted. I don't want the complete file to get sorted.
Currently All_users.txt contains the following lines.
##############
# ARS USERS
##############
mike, Mike... (6 Replies)
I am trying to parse a file but the filehas binary data inline mixed with text fields.
I tried the binutils strings function , it get the binary data out but put the char following the binary data in a new line .
input file
app_id:1936 pgm_num:0 branch:TBNY ord_num:0500012(–QMK) deal_num:0... (12 Replies)
Hi,
I have a log file that gets updated every second. Currently the size has grown to 20+ GB. I need to have a command/script, that will try to get the actual size of the file and will remove 50% of the data that are in the log file. I don't mind removing the data as the size has grown to huge... (8 Replies)
Discussion started by: Souvik Patra
8 Replies
LEARN ABOUT DEBIAN
reprof
REPROF(1) User Commands REPROF(1)NAME
reprof - predict protein secondary structure and solvent accessibility
SYNOPSIS
reprof -i [query.blastPsiMat] [OPTIONS]
reprof -i [query.fasta] [OPTIONS]
reprof -i [query.blastPsiMat|query.fasta] --mutations [mutations.txt] [OPTIONS]
DESCRIPTION
Predict protein secondary structure and solvent accessibility.
Output Format
The output format is self-explanatory, i.e. the colums of the output are described in the output file itself.
OPTIONS -i, --input=FILE
Input BLAST PSSM matrix file (from Blast -Q option) or input (single) FASTA file.
-o, --out=FILE
Either an output file or a directory. If not provided or a directory, the suffix of the input filename (i.e. .fasta or .blastPsiMat) is
replaced to create an output filename.
--mutations=[all|FILE]
Either the keyword "all" to predict all possible mutations or a file containing mutations one per line such as "C12M" for C is mutated
to M on position 12:
C30Y
R31W
G48D
This mutation code is also attached to the output filename using "_". An additional file ending "_ORI" contains the prediction using
no evolutionary information even if a BLAST PSSM matrix was provided.
--modeldir=DIR
Directory where the model and feature files are stored. Default: /usr/share/reprof.
AUTHOR
Peter Hoenigschmid hoenigschmid@rostlab.org, Burkhard Rost
EXAMPLES
Prediction from BLAST PSSM matrix for best results:
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/example.Q.reprof
Prediction from FASTA file:
reprof -i /usr/share/doc/reprof/examples/example.fasta -o /tmp/example.fasta.reprof
Prediction from BLAST PSSM matrix file using the mutation mode:
reprof -i /usr/share/doc/reprof/examples/example.Q -o /tmp/mutations_example.Q.reprof --mutations /usr/share/doc/reprof/examples/mutations.txt
# Result files for the above call are going to be:
# /tmp/mutations_example.Q.{reprof,reprof_F172P,reprof_M1Q,reprof_N34Y,reprof_ORI} - see --mutations for a description of the extensions.
COPYRIGHT
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
BUGS
https://rostlab.org/bugzilla3/enter_bug.cgi?product=reprof
SEE ALSO blast2(1)
http://rostlab.org/
1.0.1 2012-01-13 REPROF(1)