Hello Unix gurus,
I have a gzipped file where each line contains 2 street addresses in the US. What I want to do is get a count for each state that does not match.
What I have so far is:
$ gzcat matched_10_09.txt.gz |cut -c 106-107,184-185 | head -5
CTCT
CTNY
CTCT
CTFL
CTMA
This cuts... (5 Replies)
here is what i want to achieve... consider a file contains below contents. the file size is large about 60mb
cat dump.sql
INSERT INTO `table1` (`id`, `action`, `date`, `descrip`, `lastModified`) VALUES (1,'Change','2011-05-05 00:00:00','Account Updated','2012-02-10... (10 Replies)
I am a novice writing perl scripts so I'd appreciate any help you guys can offer.
I have a list of 100 words in a file (words.txt) and I need to find them in a second file (data.txt). Whenever one of these words is found I need to write that line to a third file (out.txt) and then continue... (1 Reply)
Hi,
I would like to have the length of a segment based on coordinates of its parts.
Example input file:
chr11 genes_good3.gtf aggregate_gene 1 100 gene1
chr11 genes_good3.gtf exonic_part 1 60
chr11 genes_good3.gtf exonic_part 70 100
chr11 genes_good3.gtf aggregate_gene 200 1000 gene2... (2 Replies)
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
My goal to find how many requests in 14 days from weblog server. I know to cat a weblog file to wc -l to find the... (8 Replies)
I am trying to add a condition to the below perl that will capture the GTtag and place a specific string in the last field of each line. The problem is that the GT value used is not right after the tag rather it is a few fields away. The values should always be 0/1 or 1/2 and are in bold in the... (12 Replies)
Trying to output a result that uses the data from file to combine and subtract specific lines. If $4 matches in each line then the last $6 value is added to $2 and that becomes the new$3. Each matching line in combined into one with $1 then the original $2 then the new$3 then $5. For the cases... (4 Replies)
I am trying to output a tab-delimited result that uses the data from a tab-delimited file to combine and subtract specific lines.
If $4 matches in each line then the first matching sequential $6 value is added to $2, unless the value is 1, then the original $2 is used (like in the case of line... (3 Replies)
The below awk executes as is and produces the current output. It isvery close but what Ican not seem to do is add the -exon..., the ... portion comes from $1 and the _exon is static and will never change. If there is + sign in $4 then the ... is in acending order or sequential. If there is a - in... (2 Replies)
Discussion started by: cmccabe
2 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)