say i have these many file in a directory named exam.
1)/exam/newfolder/link.txt.
2)/exam/newfolder1/
and i create a tar say exam.tar
well the problem is,
when i read the tar file i dont find any metadata about the directories,as you cannot create a tar containig empty directories.
on the... (2 Replies)
Friends,
I need help with the following in UNIX.
Merge all csv files in one folder considering only 1 header row and ignoring header of all other files.
FYI - All files are in same format and contains same headers.
Thank you (4 Replies)
Hi,
I have an input like this
1 2 3 4
2 3 4 5
4 5 6 7
I would like to count the no. of columns and print a header with a prefix "Col".
I would also like to count the no. of rows and print as first column with each line number with a prefix "Row"
So, my output would be
... (2 Replies)
Hello There...
I have a sample input file ..
number:department:amount
125:Market:125.23
126:Hardware store:434.95
127:Video store:7.45
128:Book store:14.32
129:Gasolline:16.10
I will be doing some manipulations on all the records except the header, but the header should always be... (2 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies
LEARN ABOUT DEBIAN
bp_load_gff
BP_LOAD_GFF(1p) User Contributed Perl Documentation BP_LOAD_GFF(1p)NAME
bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bp_load_gff.pl -d testdb -u user -p pw
--dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
dna1.fa dna2.fa features1.gff features2.gff ...
DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files. You must use the
exact variant of GFF described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to
allow an existing database to be overwritten.
This script uses the Bio::DB::GFF interface, and so works with all database adaptors currently supported by that module (MySQL, Oracle,
PostgreSQL soon). However, it is slow. For faster loading, see the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.
NOTES
If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.
FASTA format files are distinguished from GFF files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
On the first load of a database, you will see a number of "unknown table" errors. This is normal.
About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000, or another power of 10.
COMMAND-LINE OPTIONS
Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database.
--dsn <dsn> Data source (default dbi:mysql:test)
--adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
--user <user> Username for mysql authentication
--pass <password> Password for mysql authentication
--fasta <path> Fasta file or directory containing fasta files for the DNA
--create Force creation and initialization of database
--maxfeature Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
--group A list of one or more tag names (comma or space separated)
to be used for grouping in the 9th column.
--upgrade Upgrade existing database to current schema
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--quiet No progress reports
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_LOAD_GFF(1p)