May I paraphrase your request: You want file2's sequences to prevail and file1's sequences inserted only if there's no equivalent in file2. If so, try
with any length fasta sequences. The traiing ">" can be taken care of piping through | sed '$d' if need be. Please be aware that your desired output's "Contig_98" line is missing an "AG" at the end.
Hi, I have two files where 1 contains data and the other contains strings eg
file 1
-0.00000 0.00000 0.00000
0.00000 0.00000 0.80000
0.50000 0.50000 0.60000
0.50000 0.50000 0.20000
-0.00000 0.00000 0.40000
file 2
F F F
F F F
T T T
T T T
T T T
How to I append file2 to file 1 to... (1 Reply)
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
I have a fasta file that looks like this:
>Noname
ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT
CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG
>Noname
ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG
ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA
...
I want to... (2 Replies)
I tried to write a script ( not working) to append first value from mylist to a file called my myfirstResult and to another called mysecondResult
awk ' {print $1} >> myfirsResult ' < mylist
awk ' {print $1} >> mysecondResult ' < mylist
$ cat mylist
A 02/16/2012
B 02/19/2012
C... (3 Replies)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Hi All,
I have to append 2 lines at the end of a text file. If those 2 lines are already there then do not append else append the 2 lines to the text file.
Eg: I have a text file, file.txt
This text file might look like this,
/home/kp/make.jsp
/home/pk/model.jsp
I have to append... (1 Reply)
Hi frnds,
My requirement is I have a zip file with name say eg: test_ABC_UH_ccde2a_awdeaea_20150422.zip
within that there are subdirectories on each directory we again have .zip files and in that we have files like mama20150422.gz and so on.
Iam in need of a bash script so that it unzips... (0 Replies)
Hii,
Could someone help me to append string to the starting of all the filenames inside a directory but it should exclude .zip files and subdirectories.
Eg.
file1: test1.log
file2: test2.log
file3 test.zip
After running the script
file1: string_test1.log
file2: string_test2.log
file3:... (4 Replies)
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)