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#!/usr/bin/perl -w
#
# rename_file.pl
# A simple script for renaming sets of files
# Usage :
#
# rename_file.pl <old_pattern> <new_pattern>
#
#$* = 1;
#$/ = "";
#### last modified by Ralf Schmid 11/10/2005
#### -end added, glob instead of readdir to fix memory issues
use Getopt::Long;
use strict;
my ($file, $dir, $format, $add, $end, $txt, $help, $sub, $new_file);
my ($col, $row, $platecoords, $char, $plate, $tracenum);
GetOptions( "add=s" => \$add, # txt to add to beginning
"end=s" => \$end,
"txt=s" => \$txt, # txt to remove
"format" => \$format, # to format the trace filenames
"dir=s" => \$dir, # directory where traces are stored
"sub=s" => \$sub, # txt to substitute for above
"help" => \$help, ); # to get help
if(!($help)&&!($add)&&!($end)&&!($format)&&!($txt))
{
print "Usage : rename_files.pl <list of arguments>\n";
print " -dir <txt> - set directory of traces <dir> to <txt>\n";
print " -add <txt> - <txt> gets added to the beginning of each\n";
print " tracefile in directory <dir>\n";
print " -end <txt> - <txt> gets added to the end of each tracefile\n";
print " -txt <txt1> - <txt> gets removed from each file\n";
print " -sub <txt2> - (only with -txt set) txt1 is replaced by txt2\n";
print " -format - Traces are reformatted to correct 96 well\n";
print " nomenclature. Single digits are replaced by double\n";
print " digits and row ID set to uppercase\n";
print " In addition, if your files do not contain\n";
print " plate coordinates, but are numbered sequentially\n";
print " e.g. trace1, trace2, trace3 etc. this option will\n";
print " convert the numbers into 96 well format\n";
print " (it assumes 1-12 refer to row A columns 1-12 etc.)\n";
print " -help - Get more detailed help\n";
exit();
}
if($help)
{
print "To help with renaming the files into EGTDC style format the script\n";
print "rename_files.pl is provided.\n\n";
print "The preferred format for trace names is :\n\n";
print "\\w\\w_\\w{2,5}_\\d\\d\\w\\d\\d\n\n";
print "where \\w represents any letter or number\n";
print " \\d represents any digit\n";
print " {2,5} = minimum/maximum number of characters\n";
print "The first two letters represent the species from which the sequences were\n";
print "derived, the middle letters represent the cDNA library used to derive the\n";
print "sequences and the last digits \ letter represent the plate number and well\n";
print "coordinates (usually in 96 well format).\n\n";
print "E.g. for sequences derived from a cDNA library made from material\n";
print "derived from the adult nervous system of the earthworm Lumbricus rubellus\n";
print "library you may use :\n\nLr_adN_01A01, Lr_adN_01A02 etc.\n\n";
print "---------------------------------------------------------------------\n";
print "rename_files.pl <list of arguments>\n";
print " -dir <txt> - set directory of traces <dir> to <txt>\n";
print " -add <txt> - <txt> gets added to the beginning of each\n";
print " tracefile in directory <dir>\n";
print " -end <txt> - <txt> gets added to the end of each tracefile\n";
print " -txt <txt1> - <txt> gets removed from each file\n";
print " -sub <txt2> - (only with -txt set) txt1 is replaced by txt2\n";
print " -format - Traces are reformatted to correct 96 well\n";
print " nomenclature. Single digits are replaced by double\n";
print " digits and row ID set to uppercase\n";
print " In addition, if your files do not contain\n";
print " plate coordinates, but are numbered sequentially\n";
print " e.g. trace1, trace2, trace3 etc. this option will\n";
print " convert the numbers into 96 well format\n";
print " (it assumes 1-12 refer to row A columns 1-12 etc.)\n";
print " -help - Get this help information\n\n";
print "e.g. rename_files.pl -dir traces -add Lr_adE -txt .scf\n";
print "will take each file in the directory <traces>, add 'Lr_adE' to the front\n";
print "of the file and remove '.scf' from the filename\n";
exit();
}
my @dir;
my $workdir = `pwd`;
if(!$dir) { $dir="./"; }
if(!$sub) { $sub=""; }
chdir ("$dir");
if($add) {
@dir = glob ("*");
foreach my $file (@dir) {
print "$file\n";
if($file !~/^\./) {
$new_file=$add;
$new_file.=$file;
system("mv $file $new_file");
}
}
}
if($end) {
@dir = glob ("*");
foreach my $file (@dir) {
if($file !~/^\./) {
$new_file=$file;
$new_file.=$end;
system("mv $file $new_file");
}
}
}
if($txt) {
@dir = glob ("*");
foreach my $file (@dir) {
if($file !~/^\./) {
$new_file= $file;
$new_file=~s/$txt/$sub/g;
system ("mv $file $new_file");
}
}
}
if($format) {
@dir = glob ("*");
foreach my $file (@dir) {
if($file !~/^\./) {
$new_file= $file;
if($new_file=~/_(\d+)$/) { # Not proper coordinates - assume 1-96 = 01A01-01H12 etc
my $tracenum=$1;
$tracenum--;
$plate=1+int($tracenum/96);
$col=int((($tracenum%96)/12))+65;
$row=($tracenum%12)+1;
$char = chr($col);
$char = uc($char);
$platecoords="$plate"."$char"."$row";
print "$file $platecoords\n";
$new_file=~s/_\d+$/_$platecoords/;
}
if($new_file=~/_\d[A-Za-z]\d+$/) # Plate ID is only in single figures
{ $new_file=~s/(\d)([A-Za-z])(\d+)$/;$1$2$3/; }
if($new_file=~/([a-z])(\d+)$/) # Column ID is lowercase
{ $new_file=~s/([a-z])(\d+)$/\u$1$2/; }
if($new_file=~/([A-Z])([0-9])$/) # Row number is only in single figures
{ $new_file=~s/([A-Z])([0-9])$/$1;$2/; }
$new_file=~s/;/0/g;
system ("mv $file $new_file");
}
}
}
chdir ("$workdir");
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