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reading multiple lines
Posted by deep (deep), 24 November 2007
Hello Folks,I want to read one line at a time from File 1, read lines from File2, do some processing and write to a files.
Let me try using an example.
My File 1 looks like :
881.5372 221.3915 4 3 SIFLFKK A=0 C=0 D=0 E=0 F=2 G=0 H=0 I=1 K=2 L=1 M=0 N=0
P=0 Q=0 R=0 S=1 T=0 V=0 W=0 Y=0
856.4441 286.4886 3 2 TSLFSFR A=0 C=0 D=0 E=0 F=2 G=0 H=0 I=0 K=0 L=1 M=0 N=0
P=0 Q=0 R=1 S=2 T=1 V=0 W=0 Y=0
File 2 looks like:
7 8 881.5372 221.3915 4 3 XP_001418543.1 SIFLFKK A=0 C=0 D=0 E=0 F=2 G=0 H=0 I=1 K=2 L=1 M=0 N=0 P=0 Q=0 R=0 S=1 T=0 V=0 W=0 Y=0
10 15 856.4441 286.4886 3 3 XP_001418056.1 DIYYRK A=0 C=0 D=1 E=0 F=0 G=0 H=0 I=1 K=1 L=0 M=0 N=0 P=0 Q=0 R=1 S=0 T=0 V=0 W=0 Y=2
272 282 1285.6006 322.4073 4 3 XP_001422002.1 REHMVEMGLNA A=1 C=0 D=0 E=2 F=0 G=1 H=1 I=0 K=0 L=1 M=2 N=1 P=0 Q=0 R=1 S=0 T=0 V=1 W=0 Y=0
38 87 5277.4026 1760.1414 3 2 XP_001420476.1 YSAALVDTNGCYASQTLEVEVSWTCETSTNTAVAAAFIAFAAFCAYSFGR A=11 C=3 D=1 E=3 F=4 G=2 H=0 I=1 K=0 L=2 M=0 N=2 P=0 Q=1 R=1 S=5 T=6 V=4
W=1 Y=3
2449 2462 1496.8094 375.2095 4 3 XP_001417092.1 TPQRPGAPVNVSFK A=1 C=0 D=0 E=0 F=1 G=1 H=0 I=0 K=1 L=0 M=0 N=1 P=3 Q=1 R=1 S=1 T=1 V=2 W=0 Y=0
584 613 3135.4741 1568.7442 2 3 XP_001421161.1 AANMLSWAVNMAATKIGGPDDAHEPVDLQN A=6 C=0 D=3 E=1 F=0 G=2 H=1 I=1 K=1 L=2 M=2 N=3 P=2 Q=1 R=0 S=1 T=1 V=2 W=1 Y=0
115 170 5985.1843 2993.5993 2 3 YP_636257.1 ELTWITGVIMAVCTVSFGVTGYSLPWDQVGYWAVKIVTGVPDAIPVVGPAIVELL A=4 C=1 D=2 E=2 F=1 G=6 H=0 I=5 K=1 L=4 M=1 N=0 P=4 Q=1 R=1 S=2 T=5 V=1
1 W=3 Y=2
File1 is smaller then File2.
I need to do is :
Read first line from File1 do processing on ALL the lines in FIle2.
read second line and again do some processing on all the lines in FIle2.
I have been able to take 1 line from File1 and one line from File2, do processing, read second line from File 2 and second from File2 (In this case i have made the two files equal lines ).
I have been able to take the first line from File1 and processed All the lines in File2. However, I am just not able to processed any further, basically reading all the line in FIle 1until eof and process all the lines in FIle2.
Below is the code, This is a WORKING CODE that works for one line. The code is huge as i am doing lots of processing, If any one can point out where I am wrong or can suggest
few things it would be of great help.
Thanks Guys
open INFILE1,"<$File1";
open INFILE2,"<$File2";
while ($line1 = <INFILE1>)
{
@nonplant_fields = split /\s+/,$line1;
while ($line2 = <INFILE2>)
{
@plantfields = split /\s+/,$line2;
$count =0;
$total_count =0;
$P_count=0;
$total_P_count=0;
$NP_count =0;
$total_NP_count =0;
$nonplant_pep_seq = $nonplant_fields[4];
$nonplant_pep_seq_length = length ($nonplant_pep_seq);
$plant_pep_seq = $plantfields[7];
$plant_pep_seq_length = length ($plant_pep_seq);
DO: for ($i=5; $i<=24;$i++)
{
$NP_numbers = $nonplant_fields[$i];
#if ($line2 =~ /([ACDEFGHIKLMNPQRSTVWY]\=\d)+/)
if ($NP_numbers =~/\d/)
{
$nonplant_AA_count = $&;
}
for ($j=$i+3; $j<=27; $j++)
{
if ($plantfields[$j] =~ /\d/)
{
$plant_AA_count = $&;
and its goes on for a while...its big script. Hopefully the snap shot can give u an idea what I am doing wrong. Thanks.
Posted by admin (Graham Ellis), 24 November 2007
You need to rewind your second file each time you read a line from the first file, or store the second file in a list and keep traversing it from there. I've put a sample up athttp://www.wellho.net/mouth/1442_Reading-a-file-multiple-times-file-pointers.html
to demonstrate the principle.
Posted by deep (deep), 24 November 2007
Thanks a lot Graham!! Tried everything, just forgot to reopen the files. Thanks again.Posted by KevinAD (KevinAD), 24 November 2007
You could also use Tie::File I would think, but I am not sure how efficient it would be. Maybe use seek() too. Posted by deep (deep), 26 November 2007
Thanks Kevin, I did try using "seek", i think some where I was messing it up. I am wondering would it be possible to use $. to get the current line number instead of "tell". Is it the case when each time I am opening the file, $. will be reset or will remember the last read line from the same file?Posted by KevinAD (KevinAD), 26 November 2007
on 11/26/07 at 04:51:04, deep wrote:
|
I am pretty sure $. is reset when a file is opened (or maybe closed). You could try experimenting and see how it behaves.
Posted by admin (Graham Ellis), 26 November 2007
$. is the number of lines read since a file was last opened (hideously none-OO - latest file opening) whereas tell refers to the number of bytes into a file which is what you need for seekPosted by deep (deep), 26 November 2007
Thanks Kevin,Graham for the suggestion(s).I am having a bit problem with the script. I keep getting "out of Memory" error. I think I can narrow it down to the way I am processing the file
while ($line2 = <INFILE2>)
{
@plantfields = split /\s+/,$line2;
$plant_prot_name = $plantfields[6];
open INFILE1,"<$File1";
while ($line1 = <INFILE1>)
{
@nonplant_fields = split /\s+/,$line1;
push (@nonplant_pep_seq,$nonplant_fields[4]);
Can You suggest is some way I can optimize this part. I am looking into using "tell" and "seek". Hopefully it might do the trick.
I have designed it such a way because I am comparing and capturing many sets of data on fly from both the files. I am at a stage of rapid prototyping so at this moment not concentrating much of the performance/optimization. Just trying to get the logic right and see the results.
Posted by admin (Graham Ellis), 27 November 2007
@nonplant_pep_seq seems to cumulatives, - i.e. building up all the time - but isn't dependent on the first file in any way. It's the only memory hog I can see that you have, and I don't see the point of doing it loits of times .... unless you are adding other things in there in the code you're not showing us.Basically, you're blowing up a balloon until it bursts. Better to start letting the air our into another file.
Posted by deep (deep), 27 November 2007
I see your point Graham, thanks. Later in the code all I am doing is manipulation of the data. I am emptying the array before the next read. Hopefully this will do the job.This page is a thread posted to the opentalk forum
at www.opentalk.org.uk and
archived here for reference. To jump to the archive index please
follow this link.
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