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Full Discussion: Problem with perl ~ tr///
Top Forums Programming Problem with perl ~ tr/// Post 302359222 by fordie on Tuesday 6th of October 2009 05:02:02 AM
Old 10-06-2009
Problem with perl ~ tr///

I am trying to run the following script which is a file format converter. The frame variable in the input file has a file of 3,2,1 which needs to be 0,1,2 respectively i.e. 3 =0 etc.
I have included the tr/// function into the script to do this, however it does not seem to be working
input its
orf00002 111 974 +3 2.94
and output should be
orf00002 Glimmer3 CDS 111 974 2 + 0 note "Glimmer3 prediction" ; colour 3

However, the output is actually

orf00002 Glimmer3 CDS 111 974 2 + 18446744073709551614 note "Glimmer3 prediction" ; colour 3

I would appreciate any help as i just can't see the problem. The script does exactly what it is supposed to do without the tr/// function but with the wrong values for the frame variable

thanks in advance and the script is included below

Brian
Code:
#!/usr/bin/perl -w

while (<>) {
    /(\S+)\s+(\d+)\s+(\d+)\s+([\/+\-])(\d)\s+(\d+)/;    
    $header = $1;
    $start = $2;
    $stop = $3;
    $strand = $4;
    $frame = $5;
    $frame = ~ tr/321/012/; 
    $score = $6;
    if ($strand eq "+"){
        print "$header\tGlimmer3\tCDS\t$start\t$stop\t$score\t$strand\t$frame\tnote \"Glimmer3 prediction\" ; colour 3\n";
    }elsif ($strand eq "-"){
        print "$header\tGlimmer3\tCDS\t$stop\t$start\t$score\t$strand\t$frame\tnote \"Glimmer3 prediction\" ; colour 3\n";
    }
}


Last edited by pludi; 10-06-2009 at 06:26 AM.. Reason: code tags please....
 

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qmail-queue(8)						      System Manager's Manual						    qmail-queue(8)

NAME
qmail-queue - queue a mail message for delivery SYNOPSIS
qmail-queue DESCRIPTION
qmail-queue reads a mail message from descriptor 0. It then reads envelope information from descriptor 1. It places the message into the outgoing queue for future delivery by qmail-send. The envelope information is an envelope sender address followed by a list of envelope recipient addresses. The sender address is preceded by the letter F and terminated by a 0 byte. Each recipient address is preceded by the letter T and terminated by a 0 byte. The list of recipient addresses is terminated by an extra 0 byte. If qmail-queue sees end-of-file before the extra 0 byte, it aborts without placing the message into the queue. Every envelope recipient address should contain a username, an @ sign, and a fully qualified domain name. qmail-queue always adds a Received line to the top of the message. Other than this, qmail-queue does not inspect the message and does not enforce any restrictions on its contents. However, the recipients probably expect to see a proper header, as described in qmail-header(5). Programs included with qmail which invoke qmail-queue will invoke the contents of $QMAILQUEUE instead, if that environment variable is set. FILESYSTEM RESTRICTIONS
qmail-queue imposes two constraints on the queue structure: each mess subdirectory must be in the same filesystem as the pid directory; and each todo subdirectory must be in the same filesystem as the intd directory. EXIT CODES
qmail-queue does not print diagnostics. It exits 0 if it has successfully queued the message. It exits between 1 and 99 if it has failed to queue the message. All qmail-queue error codes between 11 and 40 indicate permanent errors: 11 Address too long. 31 Mail server permanently refuses to send the message to any recipients. (Not used by qmail-queue, but can be used by programs offering the same interface.) All other qmail-queue error codes indicate temporary errors: 51 Out of memory. 52 Timeout. 53 Write error; e.g., disk full. 54 Unable to read the message or envelope. 55 Unable to read a configuration file. (Not used by qmail-queue.) 56 Problem making a network connection from this host. (Not used by qmail-queue.) 61 Problem with the qmail home directory. 62 Problem with the queue directory. 63 Problem with queue/pid. 64 Problem with queue/mess. 65 Problem with queue/intd. 66 Problem with queue/todo. 71 Mail server temporarily refuses to send the message to any recipients. (Not used by qmail-queue.) 72 Connection to mail server timed out. (Not used by qmail-queue.) 73 Connection to mail server rejected. (Not used by qmail-queue.) 74 Connection to mail server succeeded, but communication failed. (Not used by qmail-queue.) 81 Internal bug; e.g., segmentation fault. 91 Envelope format error. SEE ALSO
addresses(5), envelopes(5), qmail-header(5), qmail-inject(8), qmail-qmqpc(8), qmail-send(8), qmail-smtpd(8) qmail-queue(8)
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