Script Perl per selezionare la migliore linea Gene Gene da Blast Risultato

Question

Ho un file enorme con output flast e ho bisogno di selezionare l'ID della query, il soggetto GI e il telaio (fondamentalmente l'intera riga) con il valore elettronico più basso che omettono le linee duplicate (omettendo tutte le altre linee con altri valori E-più elevati).Ecco come appare il file:

# BLASTX 2.2.28+
# 0 hits found
# BLASTX 2.2.28+
# Query: Tx6_c1_seq1
# Database: /mnt/swissprot
# Fields: query id, subject gi, subject title, subject length, gap opens, q. start, q. end, s. start, s. end, evalue, % subject coverage, % identity, query/sbjct frames
# 24 hits found
Tx6_c1_seq1 6439823 RecName: Full=E3 ubiquitin-protein ligase siah-1; AltName: Full=Seven in absentia homolog 1 434 1   9   173 224 282 1e-06   65  32.20   3/0
Tx6_c1_seq1 577332  RecName: Full=Putative E3 ubiquitin-protein ligase SINAT1; AltName: Full=Seven in absentia homolog 1    305 1   9   179 111 171 3e-05   67  32.79   3/0
Tx6_c1_seq1 3548505 RecName: Full=E3 ubiquitin-protein ligase siah-1; AltName: Full=Seven in absentia homolog 1 419 2   9   173 209 267 8e-05   65  32.20   3/0
Tx6_c1_seq1 577547  RecName: Full=E3 ubiquitin-protein ligase siah2; AltName: Full=Seven in absentia homolog 2; AltName: Full=Xsiah-2   313 1   15  173 125 181 2e-04   62  29.82   3/0
Tx6_c1_seq1 577417  RecName: Full=E3 ubiquitin-protein ligase Siah1; AltName: Full=Seven in absentia homolog 1; Short=Siah-1    282 1   15  173 96  152 3e-04   62  29.82   3/0
Tx6_c1_seq1 577554  RecName: Full=E3 ubiquitin-protein ligase SINAT2; AltName: Full=Seven in absentia homolog 2 308 1   9   179 114 174 4e-04   67  31.15   3/0
# BLASTX 2.2.28+
# Query: Tx_11_c0_seq1
# Database: /mnt/swissprot
# Fields: query id, subject gi, subject title, subject length, gap opens, q. start, q. end, s. start, s. end, evalue, % subject coverage, % identity, query/sbjct frames
# 1 hits found
Tx_11_c0_seq1   977285  RecName: Full=120.7 kDa protein in NOF-FB transposable element  1056    15  957 28  147 455 8e-13   79  27.81   -2/0
# BLASTX 2.2.28+
# Query: Tx_11_c1_seq1

.

L'uscita prevista in questo caso dovrebbe essere solo queste due linee poiché sono quelle con il più piccolo E_Value:

Tx6_c1_seq1 6439823 RecName: Full=E3 ubiquitin-protein ligase siah-1; AltName: Full=Seven in absentia homolog 1 434 1   9   173 224 282 1e-06   65  32.20   3/0
Tx_11_c0_seq1   977285  RecName: Full=120.7 kDa protein in NOF-FB transposable element  1056

.

Ho scritto il mio codice, ma non sembra funzionare.Potresti aiutarmi per favore per risolvere questo problema.Apprezzerei davvero il tuo tempo e aiuto.Questo è quello che ho finora:

#!/usr/bin/perl -w

# Author:
# 01/07/2014
# This script removes duplicate records from a "short" format BLAST output file, and keeps only the "best" records  (sorts by smallest e-value and then biggest percent identity)
# Usage: bestblast.pl <input file> <output file>

#-----------------------------------------------------------------------------------------------------------------------------------------
#Deal with passed parameters
#-----------------------------------------------------------------------------------------------------------------------------------------
#If no arguments are passed, show usage message and exit program.
if ($#ARGV == -1) {
    usage("BLAST BEST 1.0 2014");
    exit;
}

#get the names of the input file (first argument passed) and output file (second argument passed)
$in_file = $ARGV[0];
$out_file = $ARGV[1];

#Open the input file for reading, open the output file for writing.
#If either are unsuccessful, print an error message and exit program.
unless ( open(IN, "$in_file") ) {
    usage("Got a bad input file: $in_file");
    exit;
}
unless ( open(OUT, ">$out_file") ) {
    usage("Got a bad output file: $out_file");
    exit;
}

#Everything looks good. Print the parameters we've found.
print "Parameters:\ninput file = $in_file\noutput file = $out_file\n\n";

#-----------------------------------------------------------------------------------------------------------------------------------------
#The main event
#-----------------------------------------------------------------------------------------------------------------------------------------

$counter = 0;
$total_counter = 0;

print "De-duplicating File...\n";

@in = <IN>;

#Do stuff for each line of text in the input file.
foreach $line (@in) {
    #if the line starts with a pound symbol, it is not real data, so skip this line.
    if ( $line =~ /^#/ ) {
     next;
     }

    #Count the total number of data lines in the file.
    $total_counter++;

    #The chomp commands removes any new line (and carriage return) characters from the end of the line.
    chomp($line);

    #Split up the tab delimited line, naming only the variables we are interested in (i.e. query id, subject gi, subject title, subject length, gap opens, q. start, q. end, s. start, s. end, evalue, % subject coverage, % identity, query/sbjct frames)
    ($query_id, $subject_gi, $subject_title, $subject_length, $gap_opens, $q_start, $q_end, $s_start, $s_end, $evalue, $subject_coverage, $identity, $query_sbjct_frames) = split(/\t/, $line);

    #check to see if the id label is already in the list of ids (called dedupe)
    #if its not there, add it.
    if ( $dedupe{$query_id} ) {
    #if it is, look at the old line to see if it is still "better" than the new one.
    ($query_id, $subject_gi, $subject_title, $subject_length, $gap_opens, $q_start, $q_end, $s_start, $s_end, $list_evalue, $subject_coverage, $list_identity, $query_sbjct_frames) = split(/\t/,$dedupe{$query_id});

    #if the new evalue is better than the old one, change the value of this id to the new line.
    #otherwise, if the the new evalue is the same, and the percent_identity is better, change the value of this id to the new line.
    #otherwise, don't do anything (keep the old line).
    if ( $evalue < $list_evalue ) {
        $dedupe{$query_id} = $line;
    }
    elsif ( $evalue == $list_evalue ) {
        if ( $identity > $list_identity ) {
        $dedupe{$query_id} = $line;
        }
    }
    }
    else {
    $dedupe{$query_id} = $line;
    #count the number of non-duplicated lines we have.
    $counter++;
    }
}
print "Total # records = $total_counter\nBest only # records = $counter\n";
print "Writing to output file...\n";

#Print the final "dedupe" list to the new file (adding the new line back on the end).
foreach $query_id (sort keys %dedupe) {
    print OUT "$dedupe{$query_id}\n";
}

#Close the files.
close(IN);
close(OUT);
print "Done.\n";

#-----------------------------------------------------------------------------------------------------------------------------------------
#Subroutines
#-----------------------------------------------------------------------------------------------------------------------------------------
sub usage {
    my($message) = @_;
    print "\n$message\n";

    print "\nThis script removes duplicate records from a \"short\" format BLAST output file, and keeps only the \"best\" records.\nIt sorts by smallest e-value and then biggest percent identity.\n";
    print "Usage: bestbenter code herelast.pl <input file> <output file>\n";
    print "\n Author \n";
    print "01/07/2014\n";
}

.

Answer 1

Prova ad aggiungere "Usa rigoroso" nella parte superiore dopo la shebang - Può aiutare a localizzare qualcos'altro.

Prova a sostituire "se ($ dedupe {$ query_id})" con "se (definito ($ dedene {$ query_id}))"

Tieni presente che la maggior parte delle persone su così non sono biologi / genomisti (!) E non ho idea di cosa stai parlando, vediamo solo numeri e parole che non significano nulla per noi, quindi se riesci a spiegare meglio, possiamoessere in grado di aiutare di più.

Il seguente è più idiomatico, a proposito.

next if $line =~ /^#/;

.

Il tuo codice passa sempre dalla linea da 64 a 81. Non inserisce mai i test secondari - non trova mai duplicati.Prova a farlo nel debugger, con questo:

perl -d yourprog INFILE OUTFILE

.

Quindi eseguire ripetutamente "n" per "linea successiva".È possibile stampare valori variabili con "P Nome variabile".

Se modifico il separatore per la splitazione () dalla scheda allo spazio, ottengo questo - che ha il numero corretto di record di output almeno:

De-duplicating File...
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "AltName:" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "in" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "Full=Seven" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "absentia" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "Full=Seven" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "absentia" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "in" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "Full=Seven" isn't numeric in numeric lt (<) at ./go line 71, <IN> line 21.
Argument "homolog" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Argument "absentia" isn't numeric in numeric gt (>) at ./go line 75, <IN> line 21.
Total # records = 7
Best only # records = 2
Writing to output file...
Done.
iMac:~/tmp: more out
Tx6_c1_seq1 6439823 RecName: Full=E3 ubiquitin-protein ligase siah-1; AltName: Full=Seven in absentia homolog 1 434 1   9   173 224 282 1e-06   65  32.20   3/0
Tx_11_c0_seq1   977285  RecName: Full=120.7 kDa protein in NOF-FB transposable element  1056    15  957 28  147 455 8e-13   79  27.81   -2/0

.

Answer 2

Perché stai cercando di scrivere il tuo parser di Blast.Usa Bioperl

http://www.bioperl.org/wiki/howtoesearchio#NCBI-BLAST_PARSING_PROBLEMS

Non uso più perl più ma qui è l'idea approssimativa di cosa fare

while (my $result = $report->next_result) {
    print "Query: ".$result->query_name."\n";
    while (my $hit = $result->next_hit) {
        while ($hsp = $hit->next_hsp) {
            my evalue = $hsp->evalue;
            #convert to decimal notation
            $decimal_notation = sprintf("%.10g", $scientific_notation);

            ##... i'll leave the rest up to you
        }
     }
}

.

Answer 3

Il valore è in notazione scientifica, Perl lo tratterà come una stringa quando si fa il confronto inferiore al confronto.

Penso che avrei anche la roba deddup diversamente ...