Script Perl para seleccionar la mejor línea de gen BLAST del resultado de BLAST

Question

Tengo un archivo enorme con la salida de la explosión y necesito seleccionar la ID de consulta, el asunto GI y el cuadro (básicamente la línea completa) con el valor electrónico más bajo que omite las líneas duplicadas (omitiendo todas las demás líneas con otros valores electrónicos más altos).Así es como se ve el archivo:

# 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

La producción esperada en este caso solo debe ser estas dos líneas, ya que son las de E_Value más pequeñas:

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

Tengo mi código escrito, pero no parece funcionar.¿Podrían ustedes, por favor ayúdame a resolver este problema?Realmente apreciaría su tiempo y su ayuda.Esto es lo que tengo hasta ahora:

#!/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

Intente agregar "usar estricto" en la parte superior después del shebang, puede ayudar a localizar otra cosa.

Intente reemplazar "si ($ DEDUPE {$ QUERY_ID})" con "if (definido ($ dedupe {$ QUERY_ID}))"

Tenga en cuenta que la mayoría de las personas en los que no son biólogos / genomistas (!) Y no tienen idea de lo que está hablando, solo vemos números y palabras que no significan nada para nosotros, por lo que si puede explicarlo mejor, podemosser capaz de ayudar más.

El siguiente es más idiomático, por cierto.

next if $line =~ /^#/;

Su código siempre va de la línea 64 a 81. Nunca ingresa a las pruebas secundarias, nunca encuentra duplicados.Intente ejecutarlo en el depurador, con esto:

perl -d yourprog INFILE OUTFILE

luego haga "n" para "siguiente línea" repetidamente.Puede imprimir valores variables con "nombre de la variable P".

Si cambio el separador para la FLAME () S de Tab a espacio, obtengo esto, lo que tiene el número correcto de registros de salida al menos:

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

¿Por qué estás tratando de escribir tu propio parser explosivo?Usa BIOPERL

http://www.bioperl.org/wiki/howto: ocupa de cercaNCBI-BLAST_PARSING_PROBLEMS

Ya no uso Perl, pero aquí está la idea aproximada de qué hacer

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

El valor está en la notación científica, PERL lo tratará como una cadena al hacer menos que la comparación.

Creo que también haría las cosas deducción de manera diferente ...