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Shell Programming and Scripting
Perl to update field based on a specific set of rules
Post 303000872 by cmccabe on Friday 21st of July 2017 10:53:29 AM
07-21-2017
Code:
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\d+[+*-]|\D)(\d+)/; # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
$transcript //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10Code:
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:[+*-]d=)(\d+)/; # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
$transcript //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10In line 1 f[8] is
NM_001134408:exon3:c.415-43A>G;NM_001134407:exon3:c.415-43A>G;NM_000833:exon4:c.415-43A>G
aand the ; (semi-colon) indicates the start of a new value. NM_001134408:exon3:c.415-43A>G would be the first value, so 43 is read into the $transcript variable and since f[13] is 0.0004, f[55] is VUS. Thank you
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LEARN ABOUT OSF1
script
script(1) General Commands Manual script(1) NAME
script - Makes a transcript of terminal session SYNOPSIS
script [-a] [file] The script command makes a transcript of everything printed on your terminal. OPTIONS
Appends the transcript to file rather than writing it to file. OPERANDS
The name of an output file that will contain the transcript of the session. If this parameter is omitted, the file typescript is written. DESCRIPTION
The transcript is written to file, or appended to file if the -a option is given. If no file name is given, the transcript is saved in the file typescript. The script ends when the forked shell exits. This program is useful when you are using a CRT and want a hard-copy record of the dialog (for example, a technical writer might create an example of a working session this way). If you specify the -a option and the file does not exist, it is created. If you do not specify the -a option and the file exists, it is replaced. RESTRICTIONS
The script command requires a streams based terminal. In single user mode, streams may not be enabled. Under these circumstances, script will exit with no action. If you are the superuser and need to run this command in single user mode, use the following special instruc- tions. Enabling Streams If it is necessary to enable a streams environment in the single user mode, enter the command /sbin/init.d/streams. This command is avail- able to the superuser only. SEE ALSO
Commands: autopush(8), cat(1), echo(1), strsetup(8), tee(1) System Administration script(1)