Question

I’m not very good at this, perhaps you can help me?
I’ve successfully loaded a table into a hash, by pushing the keys and values as an array. (I realize my terminology might be incorrect, please feel free to correct it, you can see what I mean in my code below).
anyhow I’m having trouble printing the output like I want it. My objective is to make a separate file for each key, in fasta format(see below). Any Ideas?

Input:
a table:

Rank    Query Name  E-Value Frame   Description Accession (to NCBI) Bits    Fraction Identical (%)  Fraction Conserved (%)  HSP Length  Query Length    Hit Length  Coverage Query (%)  Coverage Hit (%)    Query Start Query End   Hit Start   Hit End Query String
1   50085564    4e-16   0   rank=0087540 x=1133.0 y=3620.5 length=437   GXEIR0201C1TW2  76.1    60.3174603174603    77.7777777777778    63  149 437 42.2818791946309    14.41647597254  87  149 186 372 YDKANAFLNHGNYLAYGLAATTLWVLGIPHGFAVMHGKTRRGALVFDVADLVKDALVLPWAFI
2   50085564    7e-16   0   rank=0408491 x=1798.0 y=287.0 length=296    GX6ON9A01EN42P  74.8    62.7118644067797    79.6610169491525    59  149 296 39.5973154362416    19.9324324324324    91  149 51  225 NGFLNHGNYLAYGLAATTLWVLGIPHGFAVMHGKTRRGALVFDVADLVKDALVLPWAFI
3   50085564    2e-15   0   rank=0281898 x=768.0 y=1387.0 length=283    GX6ON9A01B5QL5  72.9    63.1578947368421    80.7017543859649    57  149 283 38.255033557047 20.1413427561837    93  149 51  219 FLNHGNYLAYGLAATTLWVLGIPHGFAVMHGKTRRGALVFDVADLVKDALVLPWAFI
4   50085564    3e-15   0   rank=0714663 x=648.0 y=2458.0 length=264    GXEIR0201BU76K  72.3    59.6491228070175    80.7017543859649    57  149 264 38.255033557047 21.5909090909091    93  149 79  247 FLNHGNYLAYGLAATTLWVLGIPHGFAVMHGKTRRGALIFDVADLVKDALILPWAFI
5   50085564    3e-14   0   rank=0643198 x=1035.0 y=163.0 length=398    GXEIR0201CS5IT  69.8    61.4035087719298    78.9473684210526    57  149 398 38.255033557047 14.321608040201 93  149 147 315 FLNHGNYLAYGLAATTLWVLGIPHGFAVMXGKTRRGALVFDVADLVKDALVLPWAFI
6   50085564    4e-09   0   rank=0641162 x=178.0 y=3351.0 length=287    GXEIR0201APZFT  52.3    54.7619047619048    76.1904761904762    42  149 287 28.1879194630872    14.6341463414634    1   42  11  134 PIANTTVILLGNGTSITQAAVRMLAQAGVLIGFCGGGGTPLY
7   50085564    4e-09   0   rank=0189408 x=1683.0 y=2055.0 length=418   GXEIR0201ED2ZD  52.8    45.3333333333333    68  75  149 418 50.3355704697987    17.9425837320574    1   75  64  340 PIANTTVILLGNGTSITQAAVRMLAQAGVLIGFCGGGGTPLYMGNAIEWLTPQSEYRPTEYLQGWLGFWFDDEQRLLTAKAMQHSRIDFLQKV
8   50085564    5e-07   0   rank=0324549 x=1541.5 y=2792.5 length=281   GX6ON9A01D1MRE  45.2    75.8620689655172    89.6551724137931    29  149 281 19.4630872483221    10.3202846975089    121 149 197 281 MXGKTRRGALVFDVADLVKDALVLPWAFI
9   50085564    6e-05   0   rank=0560234 x=126.0 y=2770.0 length=351    GXEIR0201ALEM8  38.7    42.6966292134831    59.5505617977528    89  149 351 59.7315436241611    25.3561253561254    30  124 57  345 LAGFDGDGLIPALDS---SRANID---RAMKTGDLLTSEAQLTKLLYKFAARSTT*KAL/YREHDATDKANGFLNHGNYLAYGLAATTLSG\LGIPHGFAVMHGK

The output I want : in seperate files (each accesion with it’s values in a seperate file, the example below is for one of such files)

>GXEIR0201C1TW2
YDKANAFLNHGNYLAYGLAATTLWVLGIPHGFAVMHGKT\RRGALVFDVADLVKDALVLPWAFI >GXEIR0201C1TW2
NAFLNHGNYLAYGLAATTLWVLGIPHGF/AVMHGKTRRGALVFDVADLVKDALVLPWAF >GXEIR0201C1TW2
YDKANAFLNHGNYLAYGLAATTLWVLGIPHGFA*MHGKTRRGALVFDVADLVKDALVLPWAFI`

(the same for the following accession; that I call $key in my script in a seperate file)

my script so far:

#!/usr/bin/perl -w
my $infile=$ARGV[0] or die ("File not opening\n");
#### first file is a list of the reads ... you want to feed this list into a hash to pick only unique ones.
open (LIST,$infile);
my %value=();    #declare the hash
my $rank; my $query; my $evalue; my $frame; my $description; my $key; my $bits;
my$fr_ident; my $fr_cons; my $query_leng; my $hit_leng; my $query_cov; my $hit_cov; my $query_start; my $query_end; my $hit_start; my $hit_end;
my $value;my $hsp_leng;

while (<LIST>) 
{
    ($rank,$query,$evalue,$frame,$description,$key,$bits,$fr_ident,$hsp_leng,$fr_cons,$query_leng,$hit_leng,$query_cov,$hit_cov,$query_start,$query_end,$hit_start,$hit_end,$value) = split(/\t/);   # split your input by a /t and enter each into a value// might not need all of these, but good for future ref
    push (@{$value{$key}},$value);chomp (@{$value{$key}},$value); # make key and values for each entry 
}

foreach $key (sort keys %value)
{
    #print "KEY: $key , VALUE: $value , ELEMENT? \$value\{key\} :  $value{$key}\n";
    print "$key\n@{$value{$key}}\n"; #print all values of each key
    #open (OUT, ">".$infile.$key"\_primary.fasta");
}

this gives me a nice output of the key and all it’s values, I want to use the key as a new file name for my last line, and have the stuff inside the file in the output shown below…

This is after 48 hours of trying, I’m really bad at this, tried reading online stuff but I’m not following it very well.
Thanks in advance.

Answer 1

If you put an array into a string it will join the values using the special variable $" as the separator. So you’ll need to set that variable.

$" = "\n";
foreach $key (sort keys %value)
{
    open my $OUT, ">", $infile.$key."_primary.fasta";
    print $OUT "$key\n@{$value{$key}}\n";
    close $OUT;
}

Note the first arg to print() is the filehandle to print to.

An equivalent solution is to use the join() function.

foreach $key (sort keys %value)
{
    open my $OUT, ">", $infile.$key."_primary.fasta";
    print $OUT join "\n", $key, @{$value{$key}};
    print $OUT "\n";
    close $OUT;
}

print() can also take a list of items. In this case you need to set the special variable $, with the value you want as the separator for your list values. Otherwise, the values in the list will just be printed with no separator since $, is undefined by default:

$, = "\n";
foreach my $key (sort keys %value)
{
    open my $OUT, ">", $infile.$key."_primary.fasta";
    print $OUT $key, @{$value{$key}};
    print $OUT "\n";
    close $OUT;
}