Help: Content extraction

[Amy Lee]

Hello,

I have a problem while I'm processing my sequence file. The file content
is like this.

seq1 ACGGTC
ACTG
CGATCC
ACCTC
seq3

.......

And I hope make every sequence into a single file. For example, a file
"seq1" content is

seq1

ACGGTC
ACTG
And a file "seq2" content is

seq2

CGATCC
ACCTC
and so on.

However, I'm only a newbie in perl, I don't know what to do. So could
anyone post some sample codes to do that? And I don't wanna use BioPerl
because others machines do not install this package although it's quite
useful.

Thank you very much~

Regards,

Amy Lee

 

[Jürgen Exner]

I have a problem while I'm processing my sequence file.

I know text files, binary files, random access files, sequential files,
but I've never heard of a sequence file.

The file content
is like this.

......

And I hope make every sequence into a single file. For example, a file

What is a sequence?

"seq1" content is
ACGGTC
ACTG
And a file "seq2" content is
CGATCC
ACCTC
and so on.

How is this desired content different from the original content? They
seem to be identical to me.

However, I'm only a newbie in perl, I don't know what to do. So could
anyone post some sample codes to do that?

Probably not without some much improved specification.

jue

 

[Amy Lee]

Jue,

My most work is to process DNA so I save DNA sequences as a format called
FastA as you've seen before. And you could call my file dna.fasta, the
content is

seq1 ACGGTC
ACTG
CGATCC
ACCTC
seq3

.......

The "seq1" "seq2" "seq3" and "seqx" is the names of these sequences. I can
say, it's a mark. And under "seqx" it's DNA sequences. My point is quite
simple, I wanna extract every sequences as a file saved. I mean I can
extract sequences for dna.fasta and make a single file for every sequences.

There's an example.

From dna.fasta, I can make 3 sequences files and the names are from
mark names. They are seq1, seq2, seq3. In seq1, its content is

seq1

ACGGTC
ACTG
In file seq2, its content is

seq2

CGATCC
ACCTC
And so on. So from this I can deal with my sequences easily.

Thank you very much~

Regards,

Amy Lee

 

[Jürgen Exner]

My most work is to process DNA so I save DNA sequences as a format called
FastA as you've seen before. And you could call my file dna.fasta, the
content is

......

From your previous description I thought those were 3 separte files.
Obviously I was wrong.

The "seq1" "seq2" "seq3" and "seqx" is the names of these sequences. I can
say, it's a mark. And under "seqx" it's DNA sequences. My point is quite
simple, I wanna extract every sequences as a file saved. I mean I can
extract sequences for dna.fasta and make a single file for every sequences.

So you want to split the file at each ">seq*" marker.

Well, then why not just loop (while (<>)) through the input file and
whenever you encounter such a marker (m//) close() the current output
file and open() a new one?

jue

 

[John W. Krahn]

I have a problem while I'm processing my sequence file. The file content
is like this.

......

And I hope make every sequence into a single file. For example, a file
"seq1" content is
ACGGTC
ACTG
And a file "seq2" content is
CGATCC
ACCTC
and so on.

while ( <> ) {
if ( /^>(.+)/ ) {
open my $OUT, '>>', $1 or die "Cannot open '$1' $!";
select $OUT;
}
print;
}



John

 

[Amy Lee]

while ( <> ) {
if ( /^>(.+)/ ) {
open my $OUT, '>>', $1 or die "Cannot open '$1' $!";
select $OUT;
}
print;
}



John

Thank you very much~
I've solved this problem.

Regards,

Amy Lee

 

[Amy Lee]

Thank you very much~
I've solved this problem.

Regards,

Amy Lee

Anyway, could you tell me how to find out the usage of "select" function?

Thank you.

 

[Amy Lee]

From your previous description I thought those were 3 separte files.
Obviously I was wrong.


So you want to split the file at each ">seq*" marker.

Well, then why not just loop (while (<>)) through the input file and
whenever you encounter such a marker (m//) close() the current output
file and open() a new one?

jue

Yes, you are right, and the codes is right for my work.

Thank you again~

Amy

 

[Jürgen Exner]

Anyway, could you tell me how to find out the usage of "select" function?

The usage of each perl function is described in the first line(s) of the
manual page for this function. It doesn't explicitely say "Usage" as in
Unix man pages, but it has the same format:
select FILEHANDLE

Sometimes, if a function is overloaded, there may be additional usages
farther down the page, too, e.g.
select RBITS,WBITS,EBITS,TIMEOUT

jue