Re: Concatenating line into array problem
Edward Wijaya wrote:
Hi groups,
Hello,
I have a file which contain many many of this line (Fasta Format):
YNL331C
CAATATGCGAGGGACCTACATGTTGA
CATGACAATGAATTCTATTGAA
YKL071W
ATAATTATTCCTGTTTCTTTAACCTG
GTGTACAAACACTTAAGC
What I would like to do is to concatenate the line below
into one single string.
Such as the output would be:
CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGA
ATAATTATTCCTGTTTCTTTAACCTGGTGTACAAACACTTAAGC
The current code I created now seem to work but doesn't
gie the result I want. Since it concatenates all into 1 single line.
I thought there must be a very simple way to do this.
But I can't seem to figure out how to achieve that.
#---My Code --
while () {
if (/^/) {
next;
}
chomp;
$line .= $_;
}
push (@crseq, $line);
print join(\n, @crseq), \n;
This should do what you want:
$/ = '';
while ( ) {
next unless s/\s+\S.*//;
chomp;
tr/\n//d;
print $_\n;
}
John
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Re: Concatenating line into array problem
John W. Krahn wrote:
This should do what you want:
$/ = '';
while ( ) {
next unless s/\s+\S.*//;
chomp;
tr/\n//d;
print $_\n;
}
After seeing your data file change that to:
$/ = '';
while ( ) {
next unless s/\S+.*\n//;
chomp;
tr/\n//d;
print $_\n;
}
John
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Re: Concatenating line into array problem
This works:
---BEGIN CODE---
#!/usr/bin/perl
use warnings;
use strict;
$/ = '';
while (DATA) {
s/(.*?\n.*?)\n/$1/s;
print;
}
__DATA__
YNL331C
CAATATGCGAGGGACCTACATGTTGA
CATGACAATGAATTCTATTGAA
YKL071W
ATAATTATTCCTGTTTCTTTAACCTG
GTGTACAAACACTTAAGC
---END CODE---
Please check your data for the first line:
my line: CAATATGCGAGGGACCTACATGTTGACATGACAATGAATTCTATTGAA
your line: CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGA
^
An extra G has been inserted into your output would be line denoted by the
^ above and an A deleted from the end of the line. I think my line is
correct but will not swear to it.
:-)
-ZO
Edward Wijaya [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Hi groups,
I have a file which contain many many of this line (Fasta Format):
YNL331C
CAATATGCGAGGGACCTACATGTTGA
CATGACAATGAATTCTATTGAA
YKL071W
ATAATTATTCCTGTTTCTTTAACCTG
GTGTACAAACACTTAAGC
What I would like to do is to concatenate the line below
into one single string.
Such as the output would be:
CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGA
ATAATTATTCCTGTTTCTTTAACCTGGTGTACAAACACTTAAGC
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Concatenating line into array problem
Hi groups,
I have a file which contain many many of this line (Fasta Format):
YNL331C
CAATATGCGAGGGACCTACATGTTGA
CATGACAATGAATTCTATTGAA
YKL071W
ATAATTATTCCTGTTTCTTTAACCTG
GTGTACAAACACTTAAGC
What I would like to do is to concatenate the line below
into one single string.
Such as the output would be:
CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGA
ATAATTATTCCTGTTTCTTTAACCTGGTGTACAAACACTTAAGC
The current code I created now seem to work but doesn't
gie the result I want. Since it concatenates all into 1 single line.
I thought there must be a very simple way to do this.
But I can't seem to figure out how to achieve that.
Your advice is very much appreciated.
Thanks so much for your time.
--
Regards,
Edward WIJAYA
SINGAPORE
#---My Code --
while () {
if (/^/) {
next;
}
chomp;
$line .= $_;
}
push (@crseq, $line);
print join(\n, @crseq), \n;
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RE: Concatenating line into array problem
This might be closer to what you want. Just push the line onto the
array every time you come to the '' character. You'll get one empty
line at the beginning, that's why I put the shift line in.
while () {
if (/^/) {
push (@crseq, $line);
next;
}
chomp;
$line .= $_;
}
shift @crseq;
print join(\n, @crseq), \n;
-Original Message-
From: Edward Wijaya [mailto:[EMAIL PROTECTED]
Sent: Thursday, June 10, 2004 9:09 PM
To: [EMAIL PROTECTED]
Subject: Concatenating line into array problem
snip
What I would like to do is to concatenate the line below into one
single string.
Such as the output would be:
CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGA
ATAATTATTCCTGTTTCTTTAACCTGGTGTACAAACACTTAAGC
snip
#---My Code --
while () {
if (/^/) {
next;
}
chomp;
$line .= $_;
}
push (@crseq, $line);
print join(\n, @crseq), \n;
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Re: Concatenating line into array problem
On Thu, 10 Jun 2004 21:19:17 -0700, Tim Johnson [EMAIL PROTECTED]
wrote:
while () {
if (/^/) {
push (@crseq, $line);
next;
}
chomp;
$line .= $_;
}
shift @crseq;
print join(\n, @crseq), \n;
Thanks so much for your reply Tim.
But the outoput it gives is
CAATATGCGAGGGACCTACATGTTGACATGACAATGAATTCTATTGAA
instead of:
CAATATGCGAGGGACCTACATGTTGACATGACAATGAATTCTATTGAA
and
ATAATTATTCCTGTTTCTTTAACCTGGTGTACAAACACTTAAGC
So it missed out second '' part of the fasta file.
Any clue?
Thanks again before hand.
Regards
Edward WIJAYA
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RE: Concatenating line into array problem
From: Edward Wijaya mailto:[EMAIL PROTECTED] wrote:
: #---My Code --
: while () {
: if (/^/) {
: next;
: }
: chomp;
: $line .= $_;
: }
: push (@crseq, $line);
: print join(\n, @crseq), \n;
How about:
my @crseq;
while ( ) {
next unless/^[ACGT]/;
chomp;
push @crseq, $_ . scalar ;
}
print @crseq;
HTH,
Charles K. Clarkson
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Re: Concatenating line into array problem
How about:
my @crseq;
while ( ) {
next unless/^[ACGT]/;
chomp;
push @crseq, $_ . scalar ;
}
print @crseq;
Hi Charles,
Thanks for your reply.
Your code works for my example in email, but not the file
with more lines, (please see attached file).
So sorry if I didn't give precise example.
Regards,
Edward WIJAYA
YAP_up800.fasta
Description: Binary data
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RE: Concatenating line into array problem
From: Edward Wijaya mailto:[EMAIL PROTECTED] wrote:
:: How about:
::
:: my @crseq;
:: while ( ) {
:: next unless/^[ACGT]/;
:: chomp;
:: push @crseq, $_ . scalar ;
:: }
:: print @crseq;
::
:
: Hi Charles,
:
: Thanks for your reply.
:
: Your code works for my example in email, but not the file
: with more lines, (please see attached file).
:
: So sorry if I didn't give precise example.
Well, be that way!
my @crseq;
while ( ) {
# start new line
push @crseq, '' if /^/;
# kill the line ending
chomp;
# concatenate current line
# to the last array item
$crseq[-1] .= $_
}
print $_\n foreach @crseq;
HTH,
Charles K. Clarkson
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