Request to provide changes in code according to output

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November 30th, 2012, 04:00 AM

manigrover

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Join Date: May 2012

Posts: 60

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Request to provide changes in code according to output

Hi all

I have attached my sample input file and sample expected output file from my big files.

I am using following code but there are certain changes which has to be made to completely get expected output

PHP Code:


		
			
#!/usr/bin/perl -w 



use strict; 



if ($#ARGV < 1) { 

print "Usage: $0 input_file output_file\n"; 

exit 0; 

} 



my $input_file = $ARGV[0]; 

my $output_file = $ARGV[1]; 



my $prev_ttds_num = ''; 

my @diseases = (); 

my $drug_name = ''; 



open my $IFH, '<', $input_file or die "$!\n"; 

open my $OFH, '>', $output_file or die "$!\n"; 



while (my $line = <$IFH>) { 

chomp $line; 

next if $line eq ''; 

my @array = split /\t/, $line; 



my $ttds_num = shift @array; 

my $rec_type = shift @array; 



if ($ttds_num ne $prev_ttds_num) { 

if ($prev_ttds_num ne '') { 

dump_data($OFH, $drug_name, \@diseases); 

} 

$prev_ttds_num = $ttds_num; 

@diseases = (); 

$drug_name = ''; 

} 



if ($rec_type eq 'Name') { 

$drug_name = shift @array; 

} 

elsif ($rec_type eq 'Drug(s)') { 

my $part_record = join("\t", @array); 

push @diseases, $part_record; 

} 

} 



dump_data($OFH, $drug_name, \@diseases); 

close $OFH; 

close $IFH; 



print "Done\n"; 

exit 0; 



###################################################################### 

# # 

# S U B R O U T I N E S # 

# # 

###################################################################### 



##  

# @brief Routine to dump out multiple records 

# @param FH - A file handle to write data out 

# @param drug_name - The name of the drug 

# @param disease_ref - An array references to list of disease data 

# @return undef 

# 

sub dump_data { 

my ($FH, $drug_name, $disease_ref) = @_; 

return if ($drug_name eq ''); 



foreach my $disease (@{ $disease_ref }) { 

print ${FH} "$drug_name\t$disease\n"; 

} 



return; 

}

In my attached files

input is:

PHP Code:


		
			
 TTDS00002    UniProt ID    P11229

TTDS00002    Name    Muscarinic acetylcholine receptor M1

TTDS00002    Type of target    Successful target

TTDS00002    Synonyms    M1 receptor

TTDS00002    Disease    Alzheimer's disease

TTDS00002    Disease    Bronchospasm (histamine induced)

TTDS00002    Disease    Cognitive deficits

TTDS00002    Disease    Schizophrenia

TTDS00002    Function    The muscarinic acetylcholine receptor mediates various cellular responses, including inhibition of adenylate cyclase, breakdown of phosphoinositides and modulation of potassium channels through the action of G proteins.

TTDS00002    Sequence    MNTSAPPAVSPNITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDL  WLALDYVASNASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLP  VTVMCTLYWRIYRETENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPETPPGRCCRCCRAPRLLQAYSWKEEEEEDEGSMESLTSSEGEEPGSEV  VIKMPMVDPEAQAPTKQPPRSSPNTVKRPTKKGRDRAGKGQKPRGKEQLAKRKTFSLVKEKKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLW  ELGYWLCYVNSTINPMCYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQC

TTDS00002    BioChemical Class    G-protein coupled receptor (rhodopsin family)

TTDS00002    Pathway    Calcium signaling pathway

TTDS00002    Pathway    Neuroactive ligand-receptor interaction

TTDS00002    Pathway    Regulation of actin cytoskeleton

TTDS00002    Related US Patent    6,288,068

TTDS00002    Related US Patent    6,294,554

TTDS00002    Related US Patent    6,627,645

TTDS00002    Drug(s)    Pirenzepine    DAP000492    Peptic ulcer disease    Approved

TTDS00002    Drug(s)    Glycopyrrolate    DAP001116    Anesthetic    Approved

TTDS00002    Drug(s)    Clidinium    DAP001117    Abdominal/stomach pain    Approved

TTDS00002    Drug(s)    Dicyclomine    DAP001118    Irritable bowel syndrome    Approved

TTDS00002    Drug(s)    Ethopropazine    DAP001119    Parkinson's disease    Approved

TTDS00002    Drug(s)    Cycrimine    DAP001120    Parkinson's disease    Approved

TTDS00002    Drug(s)    Benztropine    DAP001121    Parkinson's disease    Approved

TTDS00002    Drug(s)    Trihexyphenidyl    DAP001122    Parkinson's disease    Approved

TTDS00002    Drug(s)    Propantheline    DAP001123    Excessive sweating (hyperhidrosis)    Approved

TTDS00002    Drug(s)    Oxyphenonium    DAP001124    Spasm    Approved

TTDS00002    Drug(s)    Biperiden    DAP001125    Parkinson's disease    Approved

TTDS00002    Antagonist    Pirenzepine    DAP000492

TTDS00002    Antagonist    Glycopyrrolate    DAP001116

TTDS00002    Antagonist    Clidinium    DAP001117

TTDS00002    Antagonist    Dicyclomine    DAP001118

TTDS00002    Antagonist    Ethopropazine    DAP001119

TTDS00002    Antagonist    Benztropine    DAP001121

TTDS00002    Antagonist    Trihexyphenidyl    DAP001122

TTDS00002    Antagonist    Propantheline    DAP001123

TTDS00002    Antagonist    Oxyphenonium    DAP001124

TTDS00002    Antagonist    Biperiden    DAP001125

TTDS00002    Binder    Cycrimine    DAP001120

And output is

PHP Code:


		
			
 P11229    M1 receptor    Pirenzepine    Antagonist    Peptic ulcer disease        DAP000492    Approved

P11229    M1 receptor    Glycopyrrolate    Antagonist    Anesthetic        DAP001116    Approved

P11229    M1 receptor    Clidinium    Antagonist    Abdominal/stomach pain        DAP001117    Approved

P11229    M1 receptor    Dicyclomine    Antagonist    Irritable bowel syndrome        DAP001118    Approved

P11229    M1 receptor    Ethopropazine    Antagonist    Parkinson's disease        DAP001119    Approved

P11229    M1 receptor    Cycrimine    Binder    Parkinson's disease        DAP001120    Approved

P11229    M1 receptor    Benztropine    Antagonist    Parkinson's disease        DAP001121    Approved

P11229    M1 receptor    Trihexyphenidyl    Antagonist    Parkinson's disease        DAP001122    Approved

P11229    M1 receptor    Propantheline    Antagonist    Excessive sweating (hyperhidrosis)        DAP001123    Approved

P11229    M1 receptor    Oxyphenonium    Antagonist    Spasm        DAP001124    Approved

P11229    M1 receptor    Biperiden    Antagonist    Parkinson's disease        DAP001125    Approved

Attached Files

	sample input file TTD.txt (2.6 KB, 29 views)
	expected sample output .txt (916 Bytes, 38 views)

November 30th, 2012, 12:49 PM

Laurent_R

Contributing User

Join Date: Jun 2012

Posts: 502

Time spent in forums: 4 Days 18 h 51 m 13 sec
Reputation Power: 385

This looks to me as a duplicate of your previous post.

And you don't explain what you want. Please do explain it.

November 30th, 2012, 03:30 PM

manigrover

Contributing User

Join Date: May 2012

Posts: 60

Time spent in forums: 10 h 42 m 3 sec
Reputation Power: 2

Hi

Thanks for reply. I need to fetch words like agnostic antagonist binder inhibitior in front of the name of drug as mentioned in my ouput above on columns. Above mentioned output are expected output for which I have attached files as well

My current code does not give me these words as mentioned in the input vefore drug name.

Kindly check it

November 30th, 2012, 04:28 PM

Laurent_R

Contributing User

Join Date: Jun 2012

Posts: 502

Time spent in forums: 4 Days 18 h 51 m 13 sec
Reputation Power: 385

Well, there is quite a bit in your files and in you code, and it is quite late over here by now, I don't feel like trying to do it now. I will try to take a look tomorrow.

December 2nd, 2012, 06:13 AM

manigrover

Contributing User

Join Date: May 2012

Posts: 60

Time spent in forums: 10 h 42 m 3 sec
Reputation Power: 2

No problem!just let me knoq qhwn you aee able to get.Mani

Request to provide changes in code according to output

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