Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
Hi Guys,
While I was writing one shell script , I just got struck at this point.
I need to extract words from a file at some specified position and do some comparison operation and need to replace the extracted word with another word.
Eg : I like Orange very much.
I need to replace... (19 Replies)
Hi,
I am new to unix. I want to delete 2 words placed at position say for example at 23rd and 45th position in a line. I used sed but couldnt achieve this.
Example: the file contains 2 lines
12345 98765 "12345" 876
12345 98765 "64578" 876
I want to delete " placed at position 13 and 19... (4 Replies)
I have a file with thousands of sequences that looks like this:
I need to replace the headers using a second file
Thus, I will end up having the following file:
I am looking for an AWK script that I can easily plug in my current pipeline.
Any help will be greatly appreciated! (6 Replies)
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Hi,
I am unable to find the right option to extract the data in the fixed width file.
sample data
abcd1234xgyhsyshijfkfk
hujk9876 io xgla
loki8787eljuwoejroiweo
dkfj9098 dja
Search based on position 8-9="xg" and print the entire row
output
... (4 Replies)
OS : Linux 2.6x
Shell : Korn
In a single file , how can I identify all the Uniqe values at a specific character position and length of each record ,
and simultaneously SPLIT the records of the file based on each of these values and write them in seperate files .
Lets say :
a) I want to... (4 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hi,
I have a file with multiple lines(fixed width dat file). I want to search for '02' in the positions 45-46 and if available, in that lines, I need to replace value in position 359 with blank. As I am new to unix, I am not able to figure out how to do this. Can you please help me to achieve... (9 Replies)
Discussion started by: Pradhikshan
9 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)