INSDSEQGET(1) NCBI Tools User's Manual INSDSEQGET(1)NAME
insdseqget - format sequences from GenBank as an XML INSDSet
SYNOPSIS
insdseqget [-] [-d filename] [-i filename] [-m n/p/b] [-n] [-o filename] [-v]
DESCRIPTION
insdseqget retrieves biological sequence data from GenBank (according to an input list of GI accession numbers) and prints it out as an XML
INSDSet document.
OPTIONS
A summary of options is included below.
- Print usage message
-d filename
Input file name for date list (desired accessions, one per line, followed by a blank line and a list of allowed dates, also one per
line)
-i filename
Input file name for GI list (default = stdin)
-m n/p/b
Molecule type:
n Nucleotide (default)
p Protein
b Both
-n Return only new records (for which the given GI refers to an old version)
-o filename
Output file name for the XML INSDSet (default = stdout)
-v Fetch SNP Variations
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2gb(1), gbseqget(1).
NCBI 2006-04-14 INSDSEQGET(1)
Check Out this Related Man Page
GBSEQGET(1) NCBI Tools User's Manual GBSEQGET(1)NAME
gbseqget - format sequences from GenBank as an XML GBSet
SYNOPSIS
gbseqget [-] [-d filename] [-i filename] [-m n/p/b] [-n] [-o filename] [-v]
DESCRIPTION
gbseqget retrieves biological sequence data from GenBank (according to an input list of GI accession numbers) and prints it out as an XML
GBSet document.
OPTIONS
A summary of options is included below.
- Print usage message
-d filename
Input file name for date list (desired accessions, one per line, followed by a blank line and a list of allowed dates, also one per
line)
-i filename
Input file name for GI list (default = stdin)
-m n/p/b
Molecule type:
n Nucleotide (default)
p Protein
b Both
-n Return only new records (for which the given GI refers to an old version)
-o filename
Output file name for the XML GBSet (default = stdout)
-v Fetch SNP Variations
NOTES
The GBSet format is deprecated in favor of INSDSet, which you can produce by running insdseqget in place of gbseqget.
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2gb(1), insdseqget(1).
NCBI 2006-04-14 GBSEQGET(1)
hello,
can anyone tell me how to rename a filename in a script to contain the current date?
i have searched for the answer but with little success!
many thanks
rkap (4 Replies)
I have one file which first line is blank and second line has some data.
$cat filename
output:
30-MAY-07
I want to store 30-MAY-07 value in one variable.
for that I wrote
var="`head -2 filename`"
It will give that result but I want to truncate the first line which is blank.
plz help. (2 Replies)
At the command line, If I type:
%dtpad filename &
It opens up a blank dtpad window, just as if I typed:
%dtpad &
And no difference if I give it the pathname, such as:
%dtpad /here/there/filename &
No issues with passing a filename using vi, xedit, emacs, etc...
The SA indicated... (1 Reply)
I posted this in the Advanced forum, thought I'd try it here as well...
At the command line, If I type:
%dtpad filename &
It just opens up a blank dtpad window (and no error is returned), just as if I typed:
%dtpad &
And no difference if I give it the pathname, such as:
%dtpad... (1 Reply)
I like to have the date in the 2008-09-01 format at the beginning of my filenames. I then hyphenate after that and then have my filename.
I have a script that creates this for me. However, I may be working on files that already have the date format already in there and so I don't want to have a... (4 Replies)
Hey guys,
I'm doing some Perl scripting for genomic data out of GenBank files...I have to extract the name of the plant, the file name, the number of bases, and all of the genes including their starting and ending positions...for example, with this GenBank file,
LOCUS NC_010093 ... (7 Replies)
Hi all,
Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here...
Nucleotide
This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
Greetings. Iīm a biologist and I donīt have mucho knowledge on Unix/Linux, but I need to use Cygwin to change some documents from a GenBank format to a FASTA format. GenBank format goes somthing like this:
LOCUS NM_013964 2568 bp mRNA linear PRI 26-APR-2009... (2 Replies)
Dear ALL,
I would really appreciate if you could help me in reformatting a file in this way:
The file refers to a list of genetic coordinates, each lines has a score value and the associated chromosome is listed in the line starting with chrom .
If more coordinates are found, the start... (2 Replies)
hi i know this is irrelevant to the question above but i was wondering how to pt a restriction in the filename in linux. I want that it is impossible to add numbers into the filename, help will be rely great , thanx!
This posting was initially given as a reply to an unrelated thread. It has been... (2 Replies)