in reply to Re: Need Help with Maybe a Regex Issue
in thread Need Help with Maybe a Regex Issue

Ok, I got it to work (many thank again to hdb, Kenosis, and graff). I found a format from the NCBI called a GFF file worked much better for parsing. However, I couldn't get the suggested hash function to work, so my updated question is how would I get this to work using a hash instead and more resemble a Perl script than a cobbled Perl/C/something construct? As it stands, it functions, but it's inefficient and not elegant. (Truncated) Sample files also attached. EDIT: I made one more modification, I finally got the hang of using a hash. 

##gff-version 3
#!gff-spec-version 1.20
#!processor NCBI annotwriter
##sequence-region NC_001903.1 1 26498
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2
+24326
NC_001903.1    RefSeq    region    1    26498    .    +    .    ID=id0
+;Name=cp26;Dbxref=taxon:224326;Is_circular=true;gbkey=Src;genome=plas
+mid;mol_type=genomic DNA;plasmid-name=cp26;strain=B31
NC_001903.1    RefSeq    gene    46    324    .    +    .    ID=gene0;
+Name=BB_B01;Dbxref=GeneID:1194411;gbkey=Gene;locus_tag=BB_B01
NC_001903.1    RefSeq    CDS    46    324    .    +    0    ID=cds0;Na
+me=NP_046987.2;Parent=gene0;Note=catalyzes the hydrolysis of acylphos
+phate;Dbxref=Genbank:NP_046987.2,GeneID:1194411;gbkey=CDS;product=acy
+lphosphatase;protein_id=NP_046987.2;transl_table=11
NC_001903.1    RefSeq    gene    308    751    .    -    .    ID=gene1
+;Name=BB_B02;Dbxref=GeneID:1194420;gbkey=Gene;locus_tag=BB_B02
NC_001903.1    RefSeq    CDS    308    751    .    -    0    ID=cds1;N
+ame=NP_046988.1;Parent=gene1;Note=hypothetical protein%3B identified 
+by Glimmer%3B putative;Dbxref=Genbank:NP_046988.1,GeneID:1194420;gbke
+y=CDS;product=hypothetical protein;protein_id=NP_046988.1;transl_tabl
+e=11
NC_001903.1    RefSeq    gene    837    2186    .    -    .    ID=gene
+2;Name=BB_B03;Dbxref=GeneID:1194419;gbkey=Gene;locus_tag=BB_B03
NC_001903.1    RefSeq    CDS    837    2186    .    -    0    ID=cds2;
+Name=NP_046989.1;Parent=gene2;Note=hypothetical protein%3B identified
+ by Glimmer%3B putative;Dbxref=Genbank:NP_046989.1,GeneID:1194419;gbk
+ey=CDS;product=hypothetical protein;protein_id=NP_046989.1;transl_tab
+le=11
NC_001903.1    RefSeq    gene    2476    3798    .    -    .    ID=gen
+e3;Name=BB_B04;Dbxref=GeneID:1194410;gbkey=Gene;locus_tag=BB_B04
NC_001903.1    RefSeq    CDS    2476    3798    .    -    0    ID=cds3
+;Name=NP_046990.2;Parent=gene3;Note=similar to GB:U07818 PID:466474 S
+P:Q45400 percent identity: 36.93%3B identified by sequence similarity
+%3B putative;Dbxref=Genbank:NP_046990.2,GeneID:1194410;gbkey=CDS;prod
+uct=chitibiose transporter protein ChbC;protein_id=NP_046990.2;transl
+_table=11
NC_001903.1    RefSeq    gene    4084    4431    .    +    .    ID=gen
+e4;Name=BB_B05;Dbxref=GeneID:1194409;gbkey=Gene;locus_tag=BB_B05
NC_001903.1    RefSeq    CDS    4084    4431    .    +    0    ID=cds4
+;Name=NP_046991.1;Parent=gene4;Note=similar to SP:P46319 PID:895750 P
+ID:1783268 GB:AL009126 percent identity: 27.62%3B identified by seque
+nce similarity%3B putative;Dbxref=Genbank:NP_046991.1,GeneID:1194409;
+gbkey=CDS;product=chitibiose transporter protein ChbA;protein_id=NP_0
+46991.1;transl_table=11
NC_001903.1    RefSeq    gene    4482    4757    .    +    .    ID=gen
+e5;Name=BB_B06;Dbxref=GeneID:1194408;gbkey=Gene;locus_tag=BB_B06
NC_001903.1    RefSeq    CDS    4482    4757    .    +    0    ID=cds5
+;Name=NP_046992.2;Parent=gene5;Note=similar to SP:P46318 PID:895748 P
+ID:1783266 GB:AL009126 percent identity: 46.32%3B identified by seque
+nce similarity%3B putative;Dbxref=Genbank:NP_046992.2,GeneID:1194408;
+gbkey=CDS;product=chitibiose transporter protein ChbB;protein_id=NP_0
+46992.2;transl_table=11
NC_001903.1    RefSeq    gene    4769    5866    .    +    .    ID=gen
+e6;Name=BB_B07;Dbxref=GeneID:1194407;gbkey=Gene;locus_tag=BB_B07
NC_001903.1    RefSeq    CDS    4769    5866    .    +    0    ID=cds6
+;Name=NP_046993.1;Parent=gene6;Note=similar to GB:M88764 SP:Q09090 PI
+D:469166 PID:1199570 percent identity: 21.29%3B identified by sequenc
+e similarity%3B putative;Dbxref=Genbank:NP_046993.1,GeneID:1194407;gb
+key=CDS;product=alpha3-beta1 integrin-binding protein;protein_id=NP_0
+46993.1;transl_table=11
NC_001903.1    RefSeq    gene    5888    6517    .    -    .    ID=gen
+e7;Name=BB_B08;Dbxref=GeneID:1194418;gbkey=Gene;locus_tag=BB_B08;pseu
+do=true
NC_001903.1    RefSeq    gene    6677    7714    .    +    .    ID=gen
+e8;Name=BB_B09;Dbxref=GeneID:1194417;gbkey=Gene;locus_tag=BB_B09
NC_001903.1    RefSeq    CDS    6677    7714    .    +    0    ID=cds7
+;Name=NP_046995.1;Parent=gene8;Note=hypothetical protein%3B identifie
+d by Glimmer%3B putative;Dbxref=Genbank:NP_046995.1,GeneID:1194417;gb
+key=CDS;product=hypothetical protein;protein_id=NP_046995.1;transl_ta
+ble=11
NC_001903.1    RefSeq    gene    7836    8765    .    +    .    ID=gen
+e9;Name=BB_B10;Dbxref=GeneID:1194406;gbkey=Gene;locus_tag=BB_B10
NC_001903.1    RefSeq    CDS    7836    8765    .    +    0    ID=cds8
+;Name=NP_046996.1;Parent=gene9;Note=similar to GP:1655797 percent ide
+ntity: 33.68%3B identified by sequence similarity%3B putative;Dbxref=
+Genbank:NP_046996.1,GeneID:1194406;gbkey=CDS;product=hypothetical pro
+tein;protein_id=NP_046996.1;transl_table=11
NC_001903.1    RefSeq    gene    8781    9299    .    +    .    ID=gen
+e10;Name=BB_B11;Dbxref=GeneID:1194405;gbkey=Gene;locus_tag=BB_B11;pse
+udo=true
NC_001903.1    RefSeq    gene    9275    10036    .    +    .    ID=ge
+ne11;Name=BB_B12;Dbxref=GeneID:1194404;gbkey=Gene;locus_tag=BB_B12
NC_001903.1    RefSeq    CDS    9275    10036    .    +    0    ID=cds
+9;Name=NP_046998.1;Parent=gene11;Note=similar to GP:2182756 percent i
+dentity: 46.00%3B identified by sequence similarity%3B putative;Dbxre
+f=Genbank:NP_046998.1,GeneID:1194404;gbkey=CDS;product=hypothetical p
+rotein;protein_id=NP_046998.1;transl_table=11
NC_001903.1    RefSeq    gene    10104    10652    .    +    .    ID=g
+ene12;Name=BB_B13;Dbxref=GeneID:1194403;gbkey=Gene;locus_tag=BB_B13
NC_001903.1    RefSeq    CDS    10104    10652    .    +    0    ID=cd
+s10;Name=NP_046999.1;Parent=gene12;Note=similar to GB:U03641 PID:4582
+18 percent identity: 42.59%3B identified by sequence similarity%3B pu
+tative;Dbxref=Genbank:NP_046999.1,GeneID:1194403;gbkey=CDS;product=hy
+pothetical protein;protein_id=NP_046999.1;transl_table=11
NC_001903.1    RefSeq    gene    10920    11417    .    -    .    ID=g
+ene13;Name=BB_B14;Dbxref=GeneID:1194402;gbkey=Gene;locus_tag=BB_B14

[download]
BB_B10
BB_B29
BB_B18
BB_B13
BB_B14
BB_B12
BB_B04
BB_B16
BB_B22
BB_B17
BB_B27
BB_B19
BB_B07
BB_B23
BB_B09
BB_B02
BB_B28
BB_B24
BB_B03
BB_B05
BB_B06

[download]
 
#!/usr/bin/perl -w
use Data::Dumper;

my @arrayOfVals;
open(my $tmp, "<", "/Users/bioinformatics/Desktop/NC_001903.gff.txt") 
+|| die "Could not open $!";

LINE: while (<$tmp>) {
    chomp;
    next LINE if /^#/; # discard header, unneeded and will interfere
    push(@arrayOfVals, $_);
}
close($tmp);
# input each line as an array

my @tmpArray;
open (my $arrVal, "<", "/Users/bioinformatics/Desktop/cp26_dff.txt") |
+| die "Could not open $!";
while (<$arrVal>) {
    chomp;
    push(@tmpArray, $_);
}
close($arrVal);
# same as above, each line of file is match string in array

my @tmpDictKeyArray;
my @tmpDictValueArray;

for (my $k=0; $k<$#arrayOfVals; $k++) {
    $gffCompare = $arrayOfVals[$k];
    $gffDescription = $arrayOfVals[$k+1];
    # rationale: $gffCompare is the compare String, 
    # and the information I need will always follow one entry after in
+ the array
    # if match is TRUE, then entry+1 will display the information
    for (my $j=0; $j<$#tmpArray; $j++) {
        $tmpArrayVal = $tmpArray[$j];
        if ($gffCompare =~ /$tmpArrayVal/) {
            if ($gffCompare =~ /.*;locus_tag=(.*)/) {
                push(@tmpDictKeyArray, $1);
                # Assign to array for hash
                } 
            if ($gffDescription =~ /.*;Name=(.*);protein_/) {
                push(@tmpDictValueArray, $1);
                # see above
                
            }
        }
    }
}

my %hashArray;
@hashArray{@tmpDictKeyArray} = @tmpDictValueArray;

print Dumper(\%hashArray);

[download]

Replies are listed 'Best First'.
Re^3: Need Help with Maybe a Regex Issue
by tangent (Parson) on Feb 27, 2014 at 21:34 UTC
    Here is a version which may help. You do not need the next LINE bit, and the C-style loop hides a bug - you never test for the last item in @tmpArray (BB_B06). 
    my @arrayOfVals;
open(my $tmp, "<", "/Users/bioinformatics/Desktop/NC_001903.gff.txt") 
+or die "Could not open $!";
while (<$tmp>) {
    chomp;
    next if /^#/; # discard header, unneeded and will interfere
    push(@arrayOfVals, $_);
}
close($tmp);

my %hashOfKeys;
open (my $arrVal, "<", "/Users/bioinformatics/Desktop/cp26_dff.txt") o
+r die "Could not open $!";
while (<$arrVal>) {
    chomp;
    $hashOfKeys{$_} = 1;
}
close($arrVal);

my %hash;

for my $k (0 .. $#arrayOfVals -1) {
    if ($arrayOfVals[$k] =~ /.*;locus_tag=(.*)/) {
        next unless $hashOfKeys{$1};
        my $key = $1;
        if ($arrayOfVals[$k+1] =~ /.*;Name=(.*);protein_/) {
            $hash{$key} = $1;
        }
    }
}
print Dumper(\%hash);

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      I didn't see that, many thanks!

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