"; # end table &table_bottom(); ############ # START FORM ############ &table_top(); print $query->startform(); print "Check the global settings for the $database_name: MINE_Customization_File. "; print "This is the file where the manager sets values for the global variables that are used by all MINE scripts.
"; print "Check the fields used by the submit, edit, and search engine scripts: MINE_Preferences.
"; print "Summarize the best matches in blast reports: Summarize Blast Reports.
"; print "Generate a link for each entry to the 1) raw text 2) html and 3) edit form: "; print "BatchEdit
"; print "See the QUICKMINE.config file: "; print "QUICKMINE.config "; print "that is used with the "; print "QUICKMINE_script "; print "
"; # print some buttons # print the button write source code for all Page_*.cgi files print $query->submit('action','Write source for all current scripts'); # print the list ALL files button print "
Update copies of the web-viewable source code for all scripts. To add security, you may wish to restrict some of the code that gets copied into world-viewable source code made with this command. In this version, all code is viewable.
"; print $query->submit('action','List ALL non-data files'); print "
Produce a list of all the files included in this version of MINE
";
# print the list update fasta files button
print $query->submit('action','Update the fasta files (*.db.fasta) from all entries in database and update the " SELF_blast_database" file');
print $var =<
Each *.db file will be used to produce a *.db.fasta file. Only use if you have enough disk space to keep
multiple copies of your database entries. The main reason to create fasta formatted copies is that these files
can be piped into the blast interface.
A file called "SELF_blast_database" is simultaneously made. This file contains all the specified .db files
in fasta format. Use formatdb to turn this into a blast-ready database using the code in the script
make_BLAST_DATABASES.
This script can either be run from the command line, or entered into your crontab file
for automation (see crontab in the documentation to see how to do this).
TEXT
print " ";
print $query->b(@unique_tags);
@get_files = $count. $file ";
}
}
# IF "Write source for all current scripts"
if ($action eq "Write source for all current scripts") {
# get all the scripts; they all begin (by convention)
# with "Page_" and end in ".cgi"
# get all the files that start with the defined prefix Page_
$ext = "Page_";
opendir THISDIR, "." or die "can't read the files in this directory";
@database = grep /$ext/, readdir THISDIR;
closedir THISDIR;
@file = @database;
# set the count to 0, some files with start with Page, but are _source files
# we don't want to copy those to source again!
$count = 0;
foreach $file (@file) {
# some files with start with Page, but are _source files
# we don't want to copy those to source again!
if ($file !~ /_source/ && $file =~ /\.cgi/) {
# increment count for each file matching Page_*.cgi
$count++;
# take the .cgi extension off the file name
$file_source = $file;
$file_source =~ s/(\.cgi)//;
# append the _source extension instead
$file_source = $file_source."_source";
# print out all the files and the source files as they are made
# copy the .cgi manually to a new _source file
open (IN, $file) || die "Can't open the file $file for reading";
open (IN_B, ">$file_source") || die "Can't open the file $file_source for writing";
# make a system call to make the source file web-readable only (4 = read)
# (6 = read + write)
system (`chmod 644 $file_source`);
# read code file and print it to the source file
# will overwrite any existing file!
undef($line);
while ($line = $count. See the source for the $file script: $source";
} # end if ($file !~ /_source/ && $file =~ /\.cgi/) {
} # end foreach $file (@file) {
} # end if ($query->('action') eq "Write source for all current scripts") {
&table_bottom();
#################
# END PROCESS FORM
#################
# PRINT BOTTOM OF EACH WEB PAGE
# if $show_source is set to 1 show a link
# at the bottom of each script to the source
# code - pass the name of this script to the
# function in CGI-MINE.pl
if ($show_source) {
$script_name = $query->script_name();
&source ($script_name);
} # ATTACH the MINE copywrite
&mine_cp;
print $query->end_html;
#################
# END WEBPAGE
#################
#####################
# FUNCTIONS
#####################
#########################
# FUNCTION: make_fasta_files
# this function opens all the
# .db files in the same directory
# and extracts the def line (header)
# and sequence (using the function &make_fasta)
# and makes a second
# file called *.db.fasta for use in
# blasting..
#########################
# Usage: &make_fasta_files();
sub make_fasta_files {
print "A concatenated list of all fasta files can be found here: $blast_database ";
print "If you intend to use this file as a blast database, you will need to run the
formatdb (application) command $formatdb_cmd from the command line or set up a cron job to do it for you. ";
# this will be the database
open (INB, ">$blast_database") || die "couldn't open $blast_database";
print "The following file extensions were selected (set in the \"MINE_Custmization_File\" by manager)
for inclusion in the $blast_database file: ";
foreach $blast_ext (@blast_extensions) {
$ext = $blast_ext;
print "$ext ";
foreach $file (@file) {
&make_fasta($file);
}
} # end function
#########################
# FUNCTION: make_fasta
# this function opens a file
# extracts the def line (header)
# and sequence and makes a second
# file called *.db.fasta
#########################
# Usage: &make_fasta();
sub make_fasta {
open(IN, "$file") || die "couldn't open $file";
open (INA, ">$file.fasta") || die "couldn't open $file.fasta";
open (GET, "$file.fasta");
chmod 0777, "$file.fasta";
$search_query = new CGI(IN);
# get the id from the file
$id = $search_query->param('id');
# get the definition from the file
$def = $search_query->param('def');
# get the sequence from the file
$seq = $search_query->param('seq');
# wrap the sequence into lines with 70 characters
&wrap_output($seq, (length $seq), $wrapped_seq);
# write the fasta sequence to file .fasta
print INA ">File: $file ID: $id DEF: $def\n$wrapped_seq";
print INB ">File: $file ID: $id DEF: $def\n$wrapped_seq";
# print to screen a link to the file made
print "File $file.fasta made
";
print $query->endform();
&table_bottom();
#################
# END FORM
#################
#################
# PROCESS FORM
################
# get the values
$action = $query->param('action');
&table_top();
# TAKE ACTION IF A BUTTON IS PRESSED!
### IF =~ /Update the fasta files/
# Make fasta files from all entries in database
if ($action =~ /Update the fasta files/) {
&make_fasta_files();
}
### IF =~ /List ALL/)
# list ALL the files in the data if "List ALL files used by the database" button is clicked
if ($action =~ /List ALL/) {
# keep track of the defined prefixes and extensions
# can't pass wildcards to be expanded, the shell interprets them as the character "*"
# this array is simply to keep track of a list of file patterns to match, and for
# ease of printing to screen - NOTE the html tag (
) in the names!
@unique_tags = (
"Page_*.cgi (all cgi scripts; click link to start script)
",
"Page_*_source (source code for all cgi scripts)
",
"*archive* (database specific files)
",
"MINE* (extra stuff)
",
"*utility (plain perl scripts that run on command line; click link to see source)
",
"*driver (driver code for common bioinformatics modules)
"
);
print "The prefixes and extension names currently defined in this database version:
";
&get_files();
@file = @database;
push (@totalfiles, @file)
}
@file = @totalfiles;
print "
";
}