Parsing

[chandniashar]

How do I write a program in Perl to extract % of sequence identity, overlap, e-value, etc. of FASTA results.
The file is somewhat like this:

FastaSummary Table



SUBMISSION PARAMETERS
TitleSequenceDatabaseuniprot
Sequence length417Sequence typep
ProgramfastaVersion3.4t25 Sept 2, 2005
Expectation upper value10.0MatrixBL50
Sequence range1-Number of scores50
Number of alignments50Word size2
Open gap penalty-10Gap extension penalty-2
Histogramfalse


AlignmentDB:IDSourceLengthIdentity%Similar%Overlap E()
1 UNIPROT:CBPA2_RAT Carboxypeptidase A2 precursor 417
100.000 100.000 417 9.7e-176
2 UNIPROT:Q504N0_MOUSE Carboxypeptidase A2, pancr 417
93.765 98.082 417 2.1e-166
3 UNIPROT:CBPA2_HUMAN Carboxypeptidase A2 precurs 417
87.050 96.163 417 1.4e-154
4 UNIPROT:Q53XS1_HUMAN Carboxypeptidase A2 (Pancr 417
86.811 95.923 417 5.5e-154

[deep022in]

How do I write a program in Perl to extract % of sequence identity, overlap, e-value, etc. of FASTA results.
The file is somewhat like this:

FastaSummary Table



SUBMISSION PARAMETERS
TitleSequenceDatabaseuniprot
Sequence length417Sequence typep
ProgramfastaVersion3.4t25 Sept 2, 2005
Expectation upper value10.0MatrixBL50
Sequence range1-Number of scores50
Number of alignments50Word size2
Open gap penalty-10Gap extension penalty-2
Histogramfalse


AlignmentDB:IDSourceLengthIdentity%Similar%Overlap E()
1 UNIPROT:CBPA2_RAT Carboxypeptidase A2 precursor 417
100.000 100.000 417 9.7e-176
2 UNIPROT:Q504N0_MOUSE Carboxypeptidase A2, pancr 417
93.765 98.082 417 2.1e-166
3 UNIPROT:CBPA2_HUMAN Carboxypeptidase A2 precurs 417
87.050 96.163 417 1.4e-154
4 UNIPROT:Q53XS1_HUMAN Carboxypeptidase A2 (Pancr 417
86.811 95.923 417 5.5e-154

could you please eloborate on exactly what you want to extract..

[chandniashar]

could you please eloborate on exactly what you want to extract..

I want to extract this portion:
AlignmentDB:IDSourceLengthIdentity%Similar%Overlap E()
1 UNIPROT:CBPA2_RAT Carboxypeptidase A2 precursor 417
100.000 100.000 417 9.7e-176
2 UNIPROT:Q504N0_MOUSE Carboxypeptidase A2, pancr 417
93.765 98.082 417 2.1e-166
3 UNIPROT:CBPA2_HUMAN Carboxypeptidase A2 precurs 417
87.050 96.163 417 1.4e-154
4 UNIPROT:Q53XS1_HUMAN Carboxypeptidase A2 (Pancr 417
86.811 95.923 417 5.5e-154.....etc

[deep022in]

I want to extract this portion:
AlignmentDB:IDSourceLengthIdentity%Similar%Overlap E()
1 UNIPROT:CBPA2_RAT Carboxypeptidase A2 precursor 417
100.000 100.000 417 9.7e-176
2 UNIPROT:Q504N0_MOUSE Carboxypeptidase A2, pancr 417
93.765 98.082 417 2.1e-166
3 UNIPROT:CBPA2_HUMAN Carboxypeptidase A2 precurs 417
87.050 96.163 417 1.4e-154
4 UNIPROT:Q53XS1_HUMAN Carboxypeptidase A2 (Pancr 417
86.811 95.923 417 5.5e-154.....etc

==========

Hi,

i have written following code.

just change the name of the input file from demo,txt to your data file and re run it.
Let me know t he results of the same

#!/usr/bin/perl;

open(fp1,"demo.txt");

my @array;

#@array will hold the extracted pattern

my $i=0;

while(<fp1>)

{

#print "$_";

if(m/^[0-9]{1,1}[\s]{1,1}[a-zA-Z]{1,}/)

{

#print $_."\n";

$array[$i]=$_;

}

if(m/^[0-9]{1,}[\.]{1,1}[0-9]{1,1}/)

{

#print $_."\n";

$array[$i]=$_;

}

if(m/AlignmentDB:/)

{

#print "$_\n";

$array[$i]=$_;

}

$i++;

}

close(fp1);

#Finally print the content of array on

foreach my $pattern (@array)

{

print "$pattern";

}

[chandniashar]

kool thanks...

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