Re: combining data from more than one file...
On Wednesday 19 May 2004 05:25 pm, Michael Robeson wrote: Sorry, I meant to upload this script (see below). However, I have one last question. Why can't I use s/\n//g;# instead of tr/A-Za-z-//cd; in the script below? I thought it would be simpler to remove the newline characters from $_ which is all I really want to do. However, most of the time all I will see are - and letters which is why I set the tr function the way I did. Hi Mike, I'm not sure if I understand exactly what you want to do here, but if you want to remove trailing newlines only, I'd use chomp; I just couldn't figure out why the substitution function wouldn't work in this case. How am I setting it up wrong? Just guessing - could it be that you need to assign the return value of s///? Something like my $var_without_newlines = s/\n//g; ? HTH, Philipp -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/ http://learn.perl.org/first-response
Re: combining data from more than one file...
Thanks to those that helped. The code works great. Now I will practice
one honing it down to the bare essentials. Below is the final code you
all helped with.
-Thanks a million!
-Mike
Begin PERL Code
#! /usr/bin/perl -w
use strict;
use FileHandle;
my %organisms;
print Enter in a list of files to be processed:\n;
# For example:
# CytB.fasta
# NADH1.fasta
#
chomp (my @infiles = STDIN);
# TODO we should make this nice later
#my @infiles = ('genetics.txt');
print Enter in the name of the OUTFILE:\n;
chomp (my $outfile = STDIN);
open(OUTFILE, $outfile)
or die Can't open OUTFILE: $!;
foreach my $infile (@infiles) {
my $FASTA = new FileHandle;
open ($FASTA, $infile)
or die Can't open INFILE: $!;
# I moved this variable outside the while-loop
# in order to be able to assign the data in
# the nextline to the organism it belongs to
# (we're keeping track of the last start line
# that we came across here)
my $orgID;
while (defined($_ = $FASTA)) {
chomp;
print \nWorking on $_\n;
# see if this line is the start of an
# organism; the thing we´re searching for
# looks like this:
# dog
# so try to match something like
# \s* zero-to-many characters of
# optional whitespace
#the bigger-than sign
# \w+ one-to-many (word) characters
# the parenthesis around the \w+ means that
# we want to access this value later using $1
if (/\s*(\w+)/) {
$orgID = $1;
print Found a new organism start line ('$orgID')\n;
}
# or just some data belonging to the last
# organism we found
else {
print Sequence data found: $_\n;
print Appending data to $orgID\n;
# let´s check if we´ve got data for this entry
if (exists ($organisms{$orgID})) {
# TODO append the data to the hash here
$organisms{$orgID} .= $_;
}
else {
# create a new hash entry for this data
$organisms{$orgID} = $_;
}
}
}
# do not forget to close the input file
close ($FASTA)
or die could not close INFILE : $!;
}
# we've processed all input files...print the resulting hash
print \n\n;
while (my ($orgID, $sequence) = each(%organisms)) {
print OUTFILE $orgID\n$sequence\n\n;
}
END PERL CODE
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RE: combining data from more than one file...
Sorry, I meant to upload this script (see below). However, I have one
last question. Why can't I use
s/\n//g;# instead of
tr/A-Za-z-//cd;
in the script below? I thought it would be simpler to remove the
newline characters from $_ which is all I really want to do. However,
most of the time all I will see are - and letters which is why I set
the tr function the way I did.
I just couldn't figure out why the substitution function wouldn't work
in this case. How am I setting it up wrong?
-Thanks
-Mike
BEGIN PERL SCRIPT
#! /usr/bin/perl -w
use strict;
use FileHandle;
my %organisms;
print Enter in a list of files to be processed:\n;
# For example:
# CytB.fasta
# NADH1.fasta
#
chomp (my @infiles = STDIN);
print Enter in the name of the OUTFILE:\n;
chomp (my $outfile = STDIN);
open(OUTFILE, $outfile)
or die Can't open OUTFILE: $!;
foreach my $infile (@infiles) {
my $FASTA = new FileHandle;
open ($FASTA, $infile)
or die Can't open INFILE: $!;
my $orgID;
while (defined($_ = $FASTA)) {
chomp;
print \n Processing $_\n;
if (/\s*(\w+)/) {
$orgID = $1;
print Found a new organism start line ('$orgID')\n;
}
else {
tr/A-Za-z-//cd; # originally tried s/\n//g;
print Sequence data found: $_\n;
print Appending data to $orgID\n;
$organisms{$orgID} .= $_;
}
}
# do not forget to close the input file
close ($FASTA)
or die could not close INFILE : $!;
}
# we've processed all input files...print the resulting hash
print \n\n;
while (my ($orgID, $sequence) = each(%organisms)) {
print OUTFILE $orgID\n$sequence\n\n;
}
END PERL SCRIPT
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Re: combining data from more than one file...
Hi,
See code
On Tue, 18 May 2004 13:16:37 -0400, Michael Robeson [EMAIL PROTECTED]
wrote:
Ok great. Most of what you show does make sense. However, there are some
bits of code that I need further clarification with. Some bits I am able
to tell what they are doing but I do not quite know how or why they work
they way they do. I'll state these areas in the code we've got together
at this point.
Hopefully, I have copied over the bits you wrote correctly. I find this
is like learning Spanish. I can read and (roughly) get the gist of the
code. But when it comes to writing the original code on my own is when I
have trouble. I am sure this will go away when I practice more. :-)
I didn't finish everything because I just need some code explained /
clarified.
Start PERL code
#!usr/bin/perl -w
use strict;
use FileHandle;
# I am unsure of what this module is. I've tried looking it up
# in the Camel and Llama book to no avail, not enough description.
# I guess I have to figure out the whole object thing?
# write 'perldoc FileHandle' on the commandline to see
# (you can do this with (hopefully) all new modules you come across).
my %organisms;
print Enter in a list of files to be processed:\n;
# For example:
# Cytb.fasta
# NADH1.fasta
# ...
# chomp (my @infiles = STDIN);
# TODO we should make this nicer later
my @infiles = ('genetics.txt');
foreach my $infile(@infiles) {
my $FASTA = new FileHandle;
# Does the above statement tell PERL to create a new
# filehandle for each file it finds? I guess I need to understand
# what new and the module FileHandle are doing.
Right on.
open ($FASTA, $infile)
or die Can't open INFILE:$!;
#$/='' #Set input operator
my $orgID;
while (defined($_ = $FASTA)) {
# Above I am unsure of why the defined function
# helps us here? I know it has something to do with an
# expression containing a valid string, but I am unsure
# of it's function here. This is something I would have
# never thought to do. :-)
It's what
while ($FASTA)
actually do.
the defined function checks wheter $_ gets set or not.
chomp;
print \nworking on $_\n;
if (\s*(\w+)/) {
$orgID=$1;
print Found a new organism start line ('$orgID')\n;
# The above regex makes complete sense. Actually, I was going to put
# something similar to that in my original post but wasn't sure
# if this was appropriate at the time. I guess it was!
} else {
print This is just some data: $_\n;
print This data needs to be appended to the hash entry for $orgID/n;
# okay, in the above you are taking the left over
# sequence ($_) and linking it as a value to $orgID ?
This if- then else statement should do what you want. I would do it like
this instead:
$organism{$orgID} .= $_;
no if and no else just that single line. Perl will just make it work the
wat it's supposed to work; if the hashkey don't exists it gets created and
the contents of $_ is inserted in it (as a string).
if (exists ($organsims{$orgID})) {
#TODO append the data to the hash here
# I guess I would put the following to append to
# the already existing hash:
# $organism{$orgID} .= $_;
} else {
#create new hash entry for this data
$organsims{$orgID} = $_;
}
}
}
# Do not forget to close the input file
close ($FASTA)
or die Could not close INFILE: $!;
# We've processed all input files... print the resulting hash
print \n*\n;
while (my($orgID, $sequence) = each(%organisms)) {
# since I want the output as:
# cat
# actgac---cgatc-ag-cttag---acg
# dog
# actatc---actat-at-accta---atc
# I would change the print statement to:
print . $orgID\n $sequence\n;
Hmm, you're trying to do string concatenation here but in that case it
should be:
print . $orgID . \n . $sequence . \n;
but it's much easier to just do it like:
print $orgID\n$sequence\n;
}
end;
end PERL code
Thanks for all your help so far! Most of this is starting help my
thinking. I will be doing a lot more of this multi-file parsing as most
of my work entails manipulating data in several files or folders at once.
-Mike
/Johan
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RE: combining data from more than one file...
Well this is the best I could do thinking through what you said. This
is actually my first time working with hashes. Also, I am
still a PERL
newbie. So, I guess a little helpful code would go a long way. I just
can't figure out how to link the regular expressions to the hash when
searching through the multiple files. to do as you say:
That's quite good - you've got more or less all the relevant parts, we
just need to put it together. I'll try to give you some hints without
revealing the whole black magic ;-)
#!/usr/bin/perl
# This script will take separate FASTA files and combine the like
# data into one FASTA file.
#
use warnings;
use strict;
my %organisms (
$orgID = $orgSeq,
);
I'd say there´s no need to fill the hash with values at this point;
I'd just declare it like this:
my %organisms;
We'll put values into it later.
print Enter in a list of files to be processed:\n;
# For example:
# CytB.fasta
# NADH1.fasta
#
chomp (my @infiles = STDIN);
This doesn't work for me - maybe I just don't know how to use it,
but for the moment, I'd hardcode this and concentrate on the
concatenation part...
my @infiles = ('genetics.txt');
foreach $infile (@infiles) {
open (FASTA, $infile)
or die Can't open INFILE: $!;
Some small things - having set warnings and strict, perl is asking
me to declare $infile and FASTA - so for me this looks like:
my $FASTA = new FileHandle;
open ($FASTA, $infile)
or die Can't open INFILE: $!;
BTW: For this to work, you need to
use FileHandle;
on top of your code.
$/=''; #Set input operator
This is an interesting approach - I've never worked with this input
operator, but I think it might make like quite easy...
I'll do it manually (which is at least good practice ;-) ), but we
should keep this in mind.
while (FASTA) {
small stuff again:
while (defined($_ = $FASTA)) {
chomp;
# Some regular expression match here?
# something that will set, say... cat
# as the key $orgID, something similar
# to below?
# and then set the sequence as the value
# $orgSeq like below?
Yes, a regexp is a very good idea here.
Generally, you just need to distinguish between the start-lines and
the regular lines here, i.e. the ones that mark the beginning of an
organism and the ones that carry the data.
# We're searching for start-lines that look like this:
# dog
# so try to match something like
# \s* zero-to-many characters of
#optional whitespace
#the bigger-than sign
# \w+ one-to-many (word) characters
# the parenthesis around the \w+ means that
# we want to access this value later using $1
if (/\s*(\w+)/) {
print found a new organism called '$1'\n;
}
# or just some data belonging to the last
# organism we found
else {
print this is just some data : $_\n;
}
Don't worry if you don't understand this on the first look - regexes can
be quite messy, but once you get used to them, they quickly become your
best friend (for getting used to them, I can recommend very much chapter
2 of the camel book...).
Anyway - now you've got the name of the new organism in a special variable
called $1 (if this is a new organism) or the data in $_ (if it´s not).
# Do not know if or where to put the following,
# but something like:
if (exists $organisms{$orgID}) {
# somehow concatenate like data
# from the different files
}
This is completely right as well - this line of code lets you check if you
already got data of this organism...let´s think about what we want to do.
We've got an hash which should look like:
cat = funny-sequence-of-a-c-g-whatever,
dog = even-funnier-sequence-of-characters
With the code from above, we iterate over all files specified on the command
line (or hardcoded into the script), and there are two kinds of line we can
meet:
- start lines
- regular data lines
We can separate start lines from regular lines with the regexp above.
When we come across a start line, we don't have to process any data: a start
line, after all, does not contain real data, but only the name identifying
the organism to which the following data belongs.
But in order to store the data for the right organism, we should keep
track
of the last start line - I would do this by storing the last ID in a
variable
(that needs to be outside the while-loop).
So now we can do something like this:
If the new line is a start line
- store the ID
If the new line is a regular line
- append it to the current entry
Since you want to append the individual strings, you don't need to check
explicitly if the hash entry exists
Re: combining data from more than one file...
Ok great. Most of what you show does make sense. However, there are
some bits of code that I need further clarification with. Some bits I
am able to tell what they are doing but I do not quite know how or why
they work they way they do. I'll state these areas in the code we've
got together at this point.
Hopefully, I have copied over the bits you wrote correctly. I find this
is like learning Spanish. I can read and (roughly) get the gist of the
code. But when it comes to writing the original code on my own is when
I have trouble. I am sure this will go away when I practice more. :-)
I didn't finish everything because I just need some code explained /
clarified.
Start PERL code
#!usr/bin/perl -w
use strict;
use FileHandle;
# I am unsure of what this module is. I've tried looking it up
# in the Camel and Llama book to no avail, not enough description.
# I guess I have to figure out the whole object thing?
my %organisms;
print Enter in a list of files to be processed:\n;
# For example:
# Cytb.fasta
# NADH1.fasta
# ...
# chomp (my @infiles = STDIN);
# TODO we should make this nicer later
my @infiles = ('genetics.txt');
foreach my $infile(@infiles) {
my $FASTA = new FileHandle;
# Does the above statement tell PERL to create a new
# filehandle for each file it finds? I guess I need to understand
# what new and the module FileHandle are doing.
open ($FASTA, $infile)
or die Can't open INFILE:$!;
#$/='' #Set input operator
my $orgID;
while (defined($_ = $FASTA)) {
# Above I am unsure of why the defined function
# helps us here? I know it has something to do with an
# expression containing a valid string, but I am unsure
# of it's function here. This is something I would have
# never thought to do. :-)
chomp;
print \nworking on $_\n;
if (\s*(\w+)/) {
$orgID=$1;
print Found a new organism start line ('$orgID')\n;
# The above regex makes complete sense. Actually, I was going to put
# something similar to that in my original post but wasn't sure
# if this was appropriate at the time. I guess it was!
} else {
print This is just some data: $_\n;
print This data needs to be appended to the hash entry for $orgID/n;
# okay, in the above you are taking the left over
# sequence ($_) and linking it as a value to $orgID ?
if (exists ($organsims{$orgID})) {
#TODO append the data to the hash here
# I guess I would put the following to append to
# the already existing hash:
# $organism{$orgID} .= $_;
} else {
#create new hash entry for this data
$organsims{$orgID} = $_;
}
}
}
# Do not forget to close the input file
close ($FASTA)
or die Could not close INFILE: $!;
# We've processed all input files... print the resulting hash
print \n*\n;
while (my($orgID, $sequence) = each(%organisms)) {
# since I want the output as:
# cat
# actgac---cgatc-ag-cttag---acg
# dog
# actatc---actat-at-accta---atc
# I would change the print statement to:
print . $orgID\n $sequence\n;
}
end;
end PERL code
Thanks for all your help so far! Most of this is starting help my
thinking. I will be doing a lot more of this multi-file parsing as most
of my work entails manipulating data in several files or folders at
once.
-Mike
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Re: combining data from more than one file...
Quite a unique case.
If your data is no very huge I would suggest, you just first keep on
reading all data into a huge has ( key as the animal value as the data)
and then just print out the hash into files
like ( writing pseudo code is easier if written in perl :-) )
my @files = qw(file1 file2 file3);
$/=\n . '';#this way you could read one record at a time
my %alldata=();
foreach $f(@files) {
open(IN,$f) || die Couldnt open file;
while(IN){
my ($animal) = /^(.*?)\n/;
$alldata{$animal} .=$_\n\n;
}
close IN;
}
## %alldata has all the data
On Mon, 2004-05-17 at 05:20, Michael S. Robeson II wrote:
Hi all,
I am having trouble with combining data from several files, and I can't
even figure out how to get started. So, I am NOT asking for any code
(though pseudo-code is ok) as I would like to try figuring this problem
out myself. So, if anyone can give me any references or hints that
would be great.
So, here is what I am trying to do:
I have say 2 files (I'd like to do this to as many files as the user
needs):
***FILE 1***
cat
atacta--gat--acgt-
ac-ac-ggttta-ca--
dog
atgcgtatgc-atcgat-ac--ac-a-ac-a-cac
mouse
acagctagc-atgca--
acgtatgctacg--atg-
***end file 1***
***FILE 2***
mouse
aatctgatcgc-atgca--
acgtaaggctagg-
cat
atacta--gat--acgt-
ac-acacagcta--ca--
dog
atgcgtatgc-atcgat
-ac--ac-a-ac-a-cac
***end file 2***
Basically, I would like to concatenate the sequence of each
corresponding animal so that the various input files would be out put
to a file like so:
***output***
cat
atacta--gat--acgt-ac-ac-ggttta-ca--atacta--gat--acgt-ac-acacagcta--ca--
dog
atgcgtatgc-atcgat-ac--ac-a-ac-a-cacatgcgtatgc-atcgat-ac--ac-a-ac-a-cac
mouse
acagctagc-atgca--acgtatgctacg--atg-aatctgatcgc-atgca--
acgtaaggctagg-
***output end***
Notice that in the two files the data are not in the same order. So, I
am trying to figure out how to have the script figure out what the
first organism is in FILE 1( say cat in this case) and find the
corresponding cat in the other input files. Then take the sequence
data (all the cat data) from FILE 2 and concatenate it to the cat
sequence data in FILE 1 to an output file. Then it should go on to the
next organism in FILE 1 and search for that next organism in the other
files (in this case FILE 2). I do not care about the order of the data,
only that the like data is concatenated together.
Again, I do NOT want this solved for me (unless I am totally lost).
Otherwise, I'll never learn. I would just like either hints /
suggestions / pseudo code / even links to books or sites that discuss
this particular topic. Meanwhile, I am eagerly awaiting my PERL
Cookbook and I'll keep searching the web.
-Thanks!
-Mike
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combining data from more than one file...
Hi all, I am having trouble with combining data from several files, and I can't even figure out how to get started. So, I am NOT asking for any code (though pseudo-code is ok) as I would like to try figuring this problem out myself. So, if anyone can give me any references or hints that would be great. So, here is what I am trying to do: I have say 2 files (I'd like to do this to as many files as the user needs): ***FILE 1*** cat atacta--gat--acgt- ac-ac-ggttta-ca-- dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cac mouse acagctagc-atgca-- acgtatgctacg--atg- ***end file 1*** ***FILE 2*** mouse aatctgatcgc-atgca-- acgtaaggctagg- cat atacta--gat--acgt- ac-acacagcta--ca-- dog atgcgtatgc-atcgat -ac--ac-a-ac-a-cac ***end file 2*** Basically, I would like to concatenate the sequence of each corresponding animal so that the various input files would be out put to a file like so: ***output*** cat atacta--gat--acgt-ac-ac-ggttta-ca--atacta--gat--acgt-ac-acacagcta--ca-- dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cacatgcgtatgc-atcgat-ac--ac-a-ac-a-cac mouse acagctagc-atgca--acgtatgctacg--atg-aatctgatcgc-atgca-- acgtaaggctagg- ***output end*** Notice that in the two files the data are not in the same order. So, I am trying to figure out how to have the script figure out what the first organism is in FILE 1( say cat in this case) and find the corresponding cat in the other input files. Then take the sequence data (all the cat data) from FILE 2 and concatenate it to the cat sequence data in FILE 1 to an output file. Then it should go on to the next organism in FILE 1 and search for that next organism in the other files (in this case FILE 2). I do not care about the order of the data, only that the like data is concatenated together. Again, I do NOT want this solved for me (unless I am totally lost). Otherwise, I'll never learn. I would just like either hints / suggestions / pseudo code / even links to books or sites that discuss this particular topic. Meanwhile, I am eagerly awaiting my PERL Cookbook and I'll keep searching the web. -Thanks! -Mike -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/ http://learn.perl.org/first-response
combining data from more than one file...
Hi all, I am having trouble with combining data from several files, and I can't even figure out how to get started. So, I am NOT asking for any code (though pseudo-code is ok) as I would like to try figuring this problem out myself. So, if anyone can give me any references or hints that would be great. So, here is what I am trying to do: I have say 2 files (I'd like to do this to as many files as the user needs): ***FILE 1*** cat atacta--gat--acgt- ac-ac-ggttta-ca-- dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cac mouse acagctagc-atgca-- acgtatgctacg--atg- ***end file 1*** ***FILE 2*** mouse aatctgatcgc-atgca-- acgtaaggctagg- cat atacta--gat--acgt- ac-acacagcta--ca-- dog atgcgtatgc-atcgat -ac--ac-a-ac-a-cac ***end file 2*** Basically, I would like to concatenate the sequence of each corresponding animal so that the various input files would be out put to a file like so: ***output*** cat atacta--gat--acgt-ac-ac-ggttta-ca--atacta--gat--acgt-ac-acacagcta--ca-- dog atgcgtatgc-atcgat-ac--ac-a-ac-a-cacatgcgtatgc-atcgat-ac--ac-a-ac-a-cac mouse acagctagc-atgca--acgtatgctacg--atg-aatctgatcgc-atgca-- acgtaaggctagg- ***output end*** Notice that in the two files the data are not in the same order. So, I am trying to figure out how to have the script figure out what the first organism is in FILE 1( say cat in this case) and find the corresponding cat in the other input files. Then take the sequence data (all the cat data) from FILE 2 and concatenate it to the cat sequence data in FILE 1 to an output file. Then it should go on to the next organism in FILE 1 and search for that next organism in the other files (in this case FILE 2). I do not care about the order of the data, only that the like data is concatenated together. Again, I do NOT want this solved for me (unless I am totally lost). Otherwise, I'll never learn. I would just like either hints / suggestions / pseudo code / even links to books or sites that discuss this particular topic. Meanwhile, I am eagerly awaiting my PERL Cookbook and I'll keep searching the web. -Thanks! -Mike -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/ http://learn.perl.org/first-response
Re: combining data from more than one file...
* Michael S. Robeson II [EMAIL PROTECTED] [2004-05-17T07:47:57]
I am having trouble with combining data from several files, and I can't
even figure out how to get started. So, I am NOT asking for any code
(though pseudo-code is ok) as I would like to try figuring this problem
out myself. So, if anyone can give me any references or hints that
would be great.
One way to solve this problem is to create a hash, in which the keys are
the animal names and the values are the sequences, possibly in an
arrayref, possibly just cat'd together.
So, something like:
for each file
open the file
for every new animal found
add all the non-blank lines to $sequences{animal}
Is that clear-ish?
--
rjbs
pgpytVlXabRaG.pgp
Description: PGP signature
RE: combining data from more than one file...
Hi all, Hi Michael, I am having trouble with combining data from several files, and I can't even figure out how to get started. So, I am NOT asking for any code (though pseudo-code is ok) as I would like to try figuring this problem out myself. So, if anyone can give me any references or hints that would be great. That´s a good approach :-) [..] Basically, I would like to concatenate the sequence of each corresponding animal so that the various input files would be out put to a file like so: [..] Notice that in the two files the data are not in the same order. So, I am trying to figure out how to have the script figure out what the first organism is in FILE 1( say cat in this case) and find the corresponding cat in the other input files. Then take the sequence data (all the cat data) from FILE 2 and concatenate it to the cat sequence data in FILE 1 to an output file. Then it should go on to the next organism in FILE 1 and search for that next organism in the other files (in this case FILE 2). I do not care about the order of the data, only that the like data is concatenated together. If memory is not a problem (i.e. the amount of data you're processing is rather small), I would read all files into a hash and concatenate them there. Something like: - open the first file - search for the beginning of an organism (say: cat), read everything after this point - search in your hash if you already stored data of this organism - if yes, append your new sequence to the already existing data - if no, create a new key in the hash - repeat this until you run out of organisms - repeat the whole procedure until you run out of files I'd happily elaborate, but I don't want to spoil your approach of wanting to solve this by yourself. If you have any questions or need additional information, just post again. :-) Again, I do NOT want this solved for me (unless I am totally lost). Otherwise, I'll never learn. I would just like either hints / suggestions / pseudo code / even links to books or sites that discuss this particular topic. Meanwhile, I am eagerly awaiting my PERL Cookbook and I'll keep searching the web. Another good starting point might be the camel book (O`Reilly: Programming Perl)... HTH, Philipp -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/ http://learn.perl.org/first-response
Re: combining data from more than one file...
On Sun, 16 May 2004 19:50:57 -0400, Michael S. Robeson II [EMAIL PROTECTED] wrote: Hi all, Hello and Welcome to the world of bioinformatics with perl! ... I think you should take a look at bioperl since this is genome data, for this exercise it's not what you want, but if you want to do more biology whith perl (blast, interfacing with databases, easy format conversion, and so on, and so forth...). Bioperl can be found at http://www.bioperl.org/ ***FILE 1*** cat atacta--gat--acgt- ac-ac-ggttta-ca-- ... Again, I do NOT want this solved for me (unless I am totally lost). Otherwise, I'll never learn. I would just like either hints / suggestions / pseudo code / even links to books or sites that discuss this particular topic. Meanwhile, I am eagerly awaiting my PERL Cookbook and I'll keep searching the web. So this was more like a link ;) -Thanks! -Mike /Johan Viklund Ps. off-topic Next exercise (or really the one before) would be to calculate the GC-skew. /off-topic -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] http://learn.perl.org/ http://learn.perl.org/first-response
Re: combining data from more than one file...
Well this is the best I could do thinking through what you said. This
is actually my first time working with hashes. Also, I am still a PERL
newbie. So, I guess a little helpful code would go a long way. I just
can't figure out how to link the regular expressions to the hash when
searching through the multiple files. to do as you say:
***Philipp wrote:***
- open the first file
- search for the beginning of an organism (say: cat), read
everything
after this point
- search in your hash if you already stored data of this organism
- if yes, append your new sequence to the already existing data
- if no, create a new key in the hash
- repeat this until you run out of organisms
- repeat the whole procedure until you run out of files
***end***
#!/usr/bin/perl
# This script will take separate FASTA files and combine the like
# data into one FASTA file.
#
use warnings;
use strict;
my %organisms (
$orgID = $orgSeq,
);
print Enter in a list of files to be processed:\n;
# For example:
# CytB.fasta
# NADH1.fasta
#
chomp (my @infiles = STDIN);
foreach $infile (@infiles) {
open (FASTA, $infile)
or die Can't open INFILE: $!;
$/=''; #Set input operator
while (FASTA) {
chomp;
# Some regular expression match here?
# something that will set, say... cat
# as the key $orgID, something similar
# to below?
# and then set the sequence as the value
# $orgSeq like below?
# Do not know if or where to put the following,
# but something like:
if (exists $organisms{$orgID}) {
# somehow concatenate like data
# from the different files
}
# print the final Hash to an outfile?
}
yeah, I'm lost. :-)
-Mike
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