Re: Extract text from file
Andrej Kastrin wrote:
I try your code; now I try to write each potential target in a record
tab separated, like:
TI- xx HD x AB- xxx HD x #record 1
TI- yy AB x AB- xxx AB x#record 2
etc...
So \t separated within record and \n separated between records. I try with
for my $term (@terms) {
if (/$term/) {
print "$_\t";
s/\n/\t/g;
print "$_\n";
but it's not OK.
You have to do a substitution.
--
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--- Shawn
"Probability is now one. Any problems that are left are your own."
SS Heart of Gold, _The Hitchhiker's Guide to the Galaxy_
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Re: Extract text from file
Andrej Kastrin wrote:
and additional question: how does Perl know where are the input files
(while we only wrote: open (TERM, $file_terms) or die "Can't open...)?
It comes from the command line. The statements:
my $file_terms = shift;
my $file_medline = shift;
are a shorten version of:
my $file_terms = shift @ARGV;
my $file_medline = shift @ARGV;
When a Perl script starts, the command line arguments are placed in the
special array @ARGV. See `perldoc -f shift` and also see `perldoc
perlvar` and search for ARGV.
For each field:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_terms) or die "Can't open $file_terms: $!\n"; #open
list of terms
open (MEDL, $file_medline) or die "Can't open $file_medline: $!\n";
#open records file
chomp( my @terms = );
while( my $line = ){
print $line if grep { $line =~ /\b$_\b/ } @terms;
}
__END__
--
Just my 0.0002 million dollars worth,
--- Shawn
"Probability is now one. Any problems that are left are your own."
SS Heart of Gold, _The Hitchhiker's Guide to the Galaxy_
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Re: Extract text from file
Chris Charley wrote:
- Original Message - From: "Andrej Kastrin"
<[EMAIL PROTECTED]>
Newsgroups: perl.beginners
To: "Perl Beginners List"
Sent: Wednesday, December 07, 2005 12:00 PM
Subject: Extract text from file
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
ABH
HD
HDD
etc.
Then I have second file which looks like:
--
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second
file, which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = ;
chomp(my @terms = );
while (my ($pmid, $ti, $ab) = split ) {
This line doesn't work. split takes the form: split /PATTERN/,EXPR
Even if you had split stated correctly, it will not give you $pmid,
$ti, $ab in this program.
See: perldoc -f split
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
You can't use a 'for' loop as an expression for an if statement.
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't
know why (compilation error in 15th and 19th line).
I'm still learning...
Thanks for any suggestion, Andrej
I think the program below will give the results you want. Also, it
leaves the second file, $file_medline, in its original format when
printed out. Don't know if you really want to have the output lines
tab separated as in your output.
#!/usr/bin/perl
use strict;
use warnings;
open TERM, "o33.txt" or die $!;
chomp(my @terms = );
close TERM or die $!;
open MEDL, "o44.txt" or die $!;
{# enclose these statements in a block so that change to $/ is
confined to these statements
local $/ = "\n\n";# set input record separator to 1 'blank line'
while () {
for my $term (@terms) {
if (/$term/) {
print;
last; # get out of 'for' loop when the first term is
found - no need to check the rest
}
}
}
}
close MEDL or die $!;
Chris
I try your code; now I try to write each potential target in a record
tab separated, like:
TI- xx HD x AB- xxx HD x #record 1
TI- yy AB x AB- xxx AB x#record 2
etc...
So \t separated within record and \n separated between records. I try with
for my $term (@terms) {
if (/$term/) {
print "$_\t";
but it's not OK.
--
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<http://learn.perl.org/> <http://learn.perl.org/first-response>
Re: Extract text from file
Shawn Corey wrote:
Andrej Kastrin wrote:
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
ABH
HD
HDD
etc.
Then I have second file which looks like:
--
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second
file, which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = ;
while (my ($pmid, $ti, $ab) = split ) {
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't
know why (compilation error in 15th and 19th line).
I'm still learning...
So aren't the folks at BioPerl.
Question: Do you want to extract just the fields or the full record if
a field contain terms from file 1? The following will print the entire
record.
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_terms) or die "Can't open $file_terms: $!"; #open
list of terms
open (MEDL, $file_medline) or die "Can't open $file_medline: $!";
#open records file
chomp( my @terms = );
{
local $/ = "\n\n";
while( my $record = ){
print $record if grep { $record =~ /\b$_\b/ } @terms;
}
}
__END__
Answer to your question: just the fields;
and additional question: how does Perl know where are the input files
(while we only wrote: open (TERM, $file_terms) or die "Can't open...)?
Cheers, Adnrej
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Re: Extract text from file
Andrej Kastrin wrote:
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
ABH
HD
HDD
etc.
Then I have second file which looks like:
--
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second file,
which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = ;
while (my ($pmid, $ti, $ab) = split ) {
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't
know why (compilation error in 15th and 19th line).
I'm still learning...
So aren't the folks at BioPerl.
Question: Do you want to extract just the fields or the full record if a
field contain terms from file 1? The following will print the entire record.
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_terms) or die "Can't open $file_terms: $!"; #open list
of terms
open (MEDL, $file_medline) or die "Can't open $file_medline: $!"; #open
records file
chomp( my @terms = );
{
local $/ = "\n\n";
while( my $record = ){
print $record if grep { $record =~ /\b$_\b/ } @terms;
}
}
__END__
--
Just my 0.0002 million dollars worth,
--- Shawn
"Probability is now one. Any problems that are left are your own."
SS Heart of Gold, _The Hitchhiker's Guide to the Galaxy_
--
To unsubscribe, e-mail: [EMAIL PROTECTED]
For additional commands, e-mail: [EMAIL PROTECTED]
Re: Extract text from file
- Original Message -
From: "Andrej Kastrin" <[EMAIL PROTECTED]>
Newsgroups: perl.beginners
To: "Perl Beginners List"
Sent: Wednesday, December 07, 2005 12:00 PM
Subject: Extract text from file
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
ABH
HD
HDD
etc.
Then I have second file which looks like:
--
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second file,
which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = ;
chomp(my @terms = );
while (my ($pmid, $ti, $ab) = split ) {
This line doesn't work. split takes the form: split /PATTERN/,EXPR
Even if you had split stated correctly, it will not give you $pmid, $ti, $ab
in this program.
See: perldoc -f split
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
You can't use a 'for' loop as an expression for an if statement.
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't know
why (compilation error in 15th and 19th line).
I'm still learning...
Thanks for any suggestion, Andrej
I think the program below will give the results you want. Also, it leaves
the second file, $file_medline, in its original format when printed out.
Don't know if you really want to have the output lines tab separated as in
your output.
#!/usr/bin/perl
use strict;
use warnings;
open TERM, "o33.txt" or die $!;
chomp(my @terms = );
close TERM or die $!;
open MEDL, "o44.txt" or die $!;
{# enclose these statements in a block so that change to $/ is confined
to these statements
local $/ = "\n\n";# set input record separator to 1 'blank line'
while () {
for my $term (@terms) {
if (/$term/) {
print;
last; # get out of 'for' loop when the first term is
found - no need to check the rest
}
}
}
}
close MEDL or die $!;
Chris
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Extract text from file
Hello dears,
I have a file in row data format, which stores different terms (e.g.
genes) and look like:
ABH
HD
HDD
etc.
Then I have second file which looks like:
--
ID- 001 #ID number
TI- analysis of HD patients. #title of article
AB- The present article deals with HD patients. #abstract
ID- 002 #ID number
TI- In reply to analysis of HD patients. #title of article
AB- The present article deals with HDD patients. #abstract
--
etc., where the separator between records is blank line.
Now I have to extract those ID, TI and AB fields from the second file,
which involves any term in the first file.
Colleague from BioPerl mailing list helps me with the following code:
#!/usr/bin/perl
use strict;
use warnings;
my $file_terms = shift;
my $file_medline = shift;
open (TERM, $file_term) or die "Can't open TERM"; #open list of terms
open (MEDL, $file_medline) or die "Can't open MEDL"; #open records file
my @terms = ;
while (my ($pmid, $ti, $ab) = split ) {
for my $term (@terms) {
if (/$term/ for ($pmid, $ti, $ab)) {
print "$pmid\t$ti\t$ab";
}
}
}
I'm little confused now, while above example doesn't work and I don't know why
(compilation error in 15th and 19th line).
I'm still learning...
Thanks for any suggestion, Andrej
--
To unsubscribe, e-mail: [EMAIL PROTECTED]
For additional commands, e-mail: [EMAIL PROTECTED]
