11-16-2013
Hi Julio, I still see this as problematic. If you repeat the command then the second time the target files will exist and match the pattern, so they will be cat onto themselves.. I did a short test and I ended up with a very big file...
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Quick question,
File A has one line (10 charachters), File B has one line (10 charachters).
how do a concat these two files together to produce a file (File C) that has the contents of Files A + B together onto one line of 20 Charachters
if I use:
cat FileA FileB > FileC
I get the... (5 Replies)
Discussion started by: kshelluser
5 Replies
2. UNIX for Dummies Questions & Answers
Hi,
I was a typical Windows guy. Like to do things just by clicking my mouse:cool:. I got a new job now...where they are big on unix.
I am trying to wet my fingures now with unix. Haven't taken the dive yet.
I am trying to find a solution for this problem.
Please help me with some... (4 Replies)
Discussion started by: sandeep78
4 Replies
3. Shell Programming and Scripting
i have data files in different directories like /jadat
/cadat etcc... i have list of this directories in a file files.
content of files:
ja
ca
directories:
/jadat
/cadat
file in each of these directories
natt_trans_like.dat
i need to loop though each directory for a... (1 Reply)
Discussion started by: dsravan
1 Replies
4. UNIX for Dummies Questions & Answers
Hi
Can anybody tell the difference between Difference between cat , cat > , cat >> and touch command in UNIX?
Thanks (6 Replies)
Discussion started by: skyineyes
6 Replies
5. Shell Programming and Scripting
Hi all,
I have a directory with many subdirectories each named like so: KOG0001, KOG0002, ...KOG9999.
Each of these subdirectories contain a variable number two kinds of files (nuc and prot) named like so: Capitella_sp_nuc_hits.fasta (nuc) and Capitella_sp_prot_hits.fasta (prot). The... (2 Replies)
Discussion started by: kmkocot
2 Replies
6. UNIX for Dummies Questions & Answers
Hi, sometimes one wants to edit files while still seeing output of earlier commands in terminal. I've found out that cat test && cat - >> test does the trick for displaying file content and adding lines but I believe I saw a much cooler command that was also able to erase lines from files. I cannot... (6 Replies)
Discussion started by: scarleo
6 Replies
7. UNIX for Dummies Questions & Answers
I am concatenating txt-files using cat:
cat *.txt > file.dat
However, the same directory has the installation instructions included, which is also a txt file: install.txt
I currently have the install.txt file renamed to install._txt, but I prefer a solution using regular expressions.
Is there... (5 Replies)
Discussion started by: figaro
5 Replies
8. UNIX for Dummies Questions & Answers
I want to printing into two files under difference situation.
For example, file 1 name.txt
>gma-miR172a Glyma02g28845
>gma-miR1513a-3p Glyma02g15840
>gma-miR166a-5p Glyma02g15840
>gma-miR1530 Glyma02g15130
>gma-miR1507a Glyma02g01841
File 2 a.gff
Glyma01g07930 ... (4 Replies)
Discussion started by: grace_shen
4 Replies
9. Shell Programming and Scripting
I am trying to cat 3 files. They all have the same name MFExtract.txt. But, they are in 3 seperate file names. Any idea how I could cat the 3 together. It's throwing me off figuring out a way because the names are the same. I was thinking just doing a 3 cat commands with the full path names and... (2 Replies)
Discussion started by: risarose87
2 Replies
10. Shell Programming and Scripting
I am new to Linux and I am trying to cat only N files in a folder. N is dynamically given number at runtime.
If I give N as 2 then cat only 2 files in the folder
and If I give N as 5 then cat only 5 files in the folder.
Is there any way to do that? (6 Replies)
Discussion started by: KMusunuru
6 Replies
LEARN ABOUT DEBIAN
lastal
LASTAL(1) User Commands LASTAL(1)
NAME
lastal - genome-scale comparison of biological sequences
SYNOPSIS
lastal [options] lastdb-name fasta-sequence-file(s)
DESCRIPTION
Find local sequence alignments.
Score options (default settings): -r: match score (DNA: 1, protein: blosum62, 0<Q<5: 6) -q: mismatch cost (DNA: 1, protein: blosum62,
0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost (DNA: 1, pro-
tein: 2, 0<Q<5: 9) -c: unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
(max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments (x) -d: minimum
score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)
Cosmetic options (default settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
doing -o: output file -f: output format: 0=tabular, 1=maf (1)
Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity for
initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128 MiB) -u: mask lowercase during
extensions: 0=never, 1=gapless,
2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)
-w: supress repeats inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output type: 0=match counts, 1=gapless, 2=redundant
gapped, 3=gapped,
4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)
-Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,
4=prb, 5=PSSM (0)
REPORTING BUGS
Report bugs to: last (ATmark) cbrc (dot) jp
LAST home page: http://last.cbrc.jp/
lastal 199 May 2012 LASTAL(1)