Beefy Boxes and Bandwidth Generously Provided by pair Networks
Clear questions and runnable code
get the best and fastest answer
 
PerlMonks  

Comment on

( #3333=superdoc: print w/ replies, xml ) Need Help??

Hello wise monks!

I am trying to parse an xml file like the one below using the following script, and everything works well except that I cannot get the full hit description (the "Hit_def" parameter in this xml format).

What I want that output to read is "43989.cce_0262 (Cyanothece ATCC 51142)", but my output only has "(Cyanothece ATCC 51142)". I played around a bit and found that if I put non-numerical text infront of this information, then I get the entire hit description. However, I'd like to be able to retrieve it without modifying the xml file. Any suggestions?

Here is a sample of the xml input

<?xml version="1.0"?> <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://ww +w.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastx</BlastOutput_program> <BlastOutput_version>BLASTX 2.2.27+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejan +dro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, an +d David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new gen +eration of protein database search programs&quot;, Nucleic Acids Res. + 25:3389-3402.</BlastOutput_reference> <BlastOutput_db>/Applications/blast-2.2.27+/db/COG_Nov2012/protein.s +equences.v9.0</BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> <BlastOutput_query-def>HKUN3Y301D9XQX</BlastOutput_query-def> <BlastOutput_query-len>508</BlastOutput_query-len> <BlastOutput_param> <Parameters> <Parameters_matrix>BLOSUM62</Parameters_matrix> <Parameters_expect>10</Parameters_expect> <Parameters_gap-open>11</Parameters_gap-open> <Parameters_gap-extend>1</Parameters_gap-extend> <Parameters_filter>L;</Parameters_filter> </Parameters> </BlastOutput_param> <BlastOutput_iterations> <Iteration> <Iteration_iter-num>1</Iteration_iter-num> <Iteration_query-ID>Query_1</Iteration_query-ID> <Iteration_query-def>HKUN3Y301D9XQX</Iteration_query-def> <Iteration_query-len>508</Iteration_query-len> <Iteration_hits> <Hit> <Hit_num>1</Hit_num> <Hit_id>gnl|BL_ORD_ID|1515029</Hit_id> <Hit_def>43989.cce_0262 (Cyanothece ATCC 51142)</Hit_def> <Hit_accession>1515029</Hit_accession> <Hit_len>65</Hit_len> <Hit_hsps> <Hsp> <Hsp_num>1</Hsp_num> <Hsp_bit-score>40.0466</Hsp_bit-score> <Hsp_score>92</Hsp_score> <Hsp_evalue>0.00664016</Hsp_evalue> <Hsp_query-from>155</Hsp_query-from> <Hsp_query-to>253</Hsp_query-to> <Hsp_hit-from>12</Hsp_hit-from> <Hsp_hit-to>44</Hsp_hit-to> <Hsp_query-frame>-1</Hsp_query-frame> <Hsp_hit-frame>0</Hsp_hit-frame> <Hsp_identity>17</Hsp_identity> <Hsp_positive>27</Hsp_positive> <Hsp_gaps>0</Hsp_gaps> <Hsp_align-len>33</Hsp_align-len> <Hsp_qseq>LRGAICSMEHIEEALGKLKDWARKLIELLLGPR</Hsp_qseq> <Hsp_hseq>ITGAVCLMDYLEKVLEKLRELAQKLIETLLGPQ</Hsp_hseq> <Hsp_midline>+ GA+C M+++E+ L KL++ A+KLIE LLGP+</Hsp_midl +ine> </Hsp> </Hit_hsps> </Hit>

and here is the perl script:

#!/usr/local/bin/perl # Usage information #Usage: $0 -i <BLAST-report-file> -o <output-file> -n <number-of-top-h +its> -b <min_bit_score> # -t <trashed.output_queries_without_hits> use strict; use warnings; use Bio::SearchIO; use Getopt::Std;#needed for flagging parameters sub main{ my %opt; #note: colons after letter mean the flag expects an argument getopt('i:o:n:b:t:', \%opt); print "Parsing the BLAST result ...\n"; my $in = Bio::SearchIO->new(-format => 'blastxml', -file => $opt{i}); open (OUT,">$opt{o}") or die "Cannot open $opt{o}: $!"; open (OUT2,">$opt{t}") or die "Cannot open $opt{t}: $!"; open (OUT3, ">$opt{o}.header") or die "Cannot open $opt{o}.header: $!" +; # print the header info for tab-deliminated columns print OUT "query_name\tquery_length\taccession_number\tsubject_length\ +tsubject_description\tE value\tbit score\tframe\tquery_start\t"; print OUT "query_end\thit_start\thit_end\t%_conserved\t%_identical\n"; print OUT2 "query_name\tquery_length\taccession_number\tsubject_length +\tsubject_description\tE value\tbit score\tframe\tquery_start\t"; print OUT2 "query_end\thit_start\thit_end\t%_conserved\t%_identical\n" +; # extraction of information for each result recursively while ( my $result = $in->next_result ) { #prints query info for reads WITHOUT hits into -t ="bad" file if ( $result->num_hits == 0 ) { print OUT2 $result->query_description . "\t"; print OUT2 $result->query_length . "\t"; print OUT2 "No hits found\n"; } else { my $count = 0; # process each hit recursively while (my $hit = $result->next_hit) { #prints query info for reads WITH hits BELOW bit-score inp +ut value into -t = "bad" file if ( $hit->bits < $opt{b}) { print OUT2 $result->query_description . "\t"; print OUT2 $result->query_length . "\t"; print OUT2 "below bit score\n";} #prints query and other info for reads WITH hits ABOVE bit +-score input into -o = "good" file elsif ( $hit->bits >= $opt{b}) { print OUT $result->query_description . "\t"; print OUT3 $result->query_description . "\n"; print OUT $result->query_length . "\t"; print OUT $hit->accession . "\t"; print OUT $hit->length . "\t"; print OUT $hit->description . "\t"; print OUT $hit->significance . "\t"; print OUT $hit->bits . "\t"; my $hspcount = 0; # process the top HSP for the top number of hits (user + defined) into -o file while (my $hsp = $hit->next_hsp) { if ($hit->bits >= $opt{b}) { print OUT "\t\t\t\t\t\t\t", if ($hspcount > 0) +; print OUT $hsp->query->frame . "\t"; print OUT $hsp->start('query') . "\t" . $hsp-> +end('query'). "\t"; print OUT $hsp->start('hit') . "\t" . $hsp->en +d('hit') . "\t"; printf OUT "%.1f" , ($hsp->frac_conserved * 10 +0); print OUT "%\t"; printf OUT "%.1f" , ($hsp->frac_identical * 10 +0); print OUT "%\n"; $hspcount++; } } } $count++; # flow control for the number of hits needed last if ($count == $opt{n}); } } } close OUT; close OUT2; } main(); print " DONE!!!\n";

and what I put into the command line:

perl scriptname.pl -i inputfile.xml -o goodoutputfile.txt -d badoutputfile.txt -n number_of_hits_to_keep -b bit-score_cutoff

and here is the output I get from "goodoutputfile.txt"

query_name query_length accession_number subject_length su +bject_description E value bit score frame query_start +query_end hit_start hit_end %_conserved %_identical HKUN3Y301D9XQX length=508 xy=1636_1159 region=1 run=R_2012_03_16_06_53 +_48_ 508 1515029 65 (Cyanothece ATCC 51142) 0.00664016 + 40.0466 0 155 253 12 44 81.8% 51.5%

In reply to get full hit descrption from blast output (xml) by ejbiers

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • Outside of code tags, you may need to use entities for some characters:
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.
  • Log In?
    Username:
    Password:

    What's my password?
    Create A New User
    Chatterbox?
    and the web crawler heard nothing...

    How do I use this? | Other CB clients
    Other Users?
    Others chanting in the Monastery: (7)
    As of 2014-08-20 08:53 GMT
    Sections?
    Information?
    Find Nodes?
    Leftovers?
      Voting Booth?

      The best computer themed movie is:











      Results (108 votes), past polls