Dear Corona688,
Below the word by word execution of program from terminal: I have the executable set in the path:
Above options comes up when trying to execute the program from terminal. I am trying to run this program automatically so that I don't have to do this interactively for 1000 of sequences.
I really appreciate your time and response Corona688.
Regards
I've written a script (bgrep) for a more advanced grep command (& attached a cut down version below). I'm trying allow all grep options to be used, or in any combination.
The script works fine if I type say
bgrep -i -files product
it will return a non-case sensitive list of matches for... (3 Replies)
Hey guys,
I have an interactive script that is quite critical to our production environmentl thus updating it to run non-interactively is not an option.
The script takes a varying number of arguments, which it ques untill user confirm end of data entry
e.g of user input :
1
2
y ... (3 Replies)
The following bash script does not work because the java/groovy code always thinks there are four arguments even if there are only 1 or 2. As you can see from my hideous backslashes, I am using cygwin bash on windows.
export... (1 Reply)
Hi!
I have a python script that requires arguments and these arguments are file paths. This script works fine when executed like this:
/my_python_script "file_path1" "file_path2"
(i added quotes as some file names may have weird characters)
the issue happens when i launch my python script... (14 Replies)
I'm pretty new to bash scripting and I've found myself writing things like this (and the same with even more nesting):
if $CATEGORIES; then
if $LABEL_SLOTS; then
$pyth "$wd/texify_grammar.py" "$input" "$texfile" "--label-slots" "--categories" "$CATEGORY_LIST"
... (9 Replies)
I've tried to find a solution to this, but I"m stumped.
OS - RH Linux 5.9
I have a bash script <myProgram.sh> that gets executed manually and creates a small response file. I'm trying to automate the running of this script.
When myProgram.sh runs, it prompts the user to enter 2 pieces of... (13 Replies)
Hi,
I wanted to pass an argument to a bash script. So that the argument is used inside the awk command inside the bash script.
I know the noraml way of passing argument to a bash script as below :
sh myScript.sh abc
Inside the bash script i can use like this
myArg1=$1
wc $myArg
But... (8 Replies)
I have a script test.sh which reads various inputs from a user.
#!/bin/ksh
read x
read y
read z
echo x: $x y: $y z: $z
# read few more things again
read a
read b
echo a: $a b: $b
When i run this script as
test.sh << EOF
1
2
EOF (3 Replies)
Hi,
I have a requirement for creating a MQ (queue) where the inputs has to be passed as arguments.
Running the script as below
./hi.sh "Servername" "QueueManagername" "QueuecreationCommand"
cat hi.sh
echo "Welcome to $1"
runmqsc $2 < $3
But the queue creation command is... (9 Replies)
I at the moment, making a simple bash script, capable of setting up an workspace for me, so i don't have to do it manually.. Problem is though i can't seem to provide the bash script any argument, without running into my error checks, checking for input...
Here is the code:
#!/bin/bash... (7 Replies)
Discussion started by: kidi
7 Replies
LEARN ABOUT DEBIAN
fastacmd
FASTACMD(1) NCBI Tools User's Manual FASTACMD(1)NAME
fastacmd - retrieve FASTA sequences from a BLAST database
SYNOPSIS
fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t]
DESCRIPTION
fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option. An example fastacmd call would be
fastacmd -d nr -s p38398
OPTIONS
A summary of options is included below.
- Print usage message
-D N Dump the entire database in some format:
1 fasta
2 GI list
3 Accession.version list
-I Print database information only (overrides all other options)
-L start,stop
Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)
-P N Retrieve sequences with Protein Identification Group (PIG) N.
-S N Strand on subsequence (nucleotide only):
1 top (default)
2 bottom
-T Print taxonomic information for requested sequence(s)
-a Retrieve duplicate accessions
-c Use ^A ( 01) as non-redundant defline separator
-d str Database (default is nr)
-i str Input file with GIs/accessions/loci for batch retrieval
-l N Line length for sequence (default = 80)
-o filename
Output file (default = stdout)
-p type
Type of file:
G guess (default): look for protein, then nucleotide
T protein
F nucleotide
-s str Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'
-t Definition line should contain target GI only
EXIT STATUS
0 Completed successfully.
1 An error (other than those below) occurred.
2 The BLAST database was not found.
3 A search (accession, GI, or taxonomy info) failed.
4 No taxonomy database was found.
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO blast(1), /usr/share/doc/blast2/fastacmd.html.
NCBI 2005-11-04 FASTACMD(1)