Re: Protein fragment recognition!

[Alaba, Oluwafemi (IITA)]

Dear Raj,

Thanks.

Could you comment on the lines of code so that i can understand better ?

Best
On Sep 20, 2015, at 10:19 PM, Raj Barath 
<barat...@live.com<mailto:barat...@live.com>> wrote:

Hi,

Is this is what you're looking for ?

my %hash;

while( my $line = <DATA> ){
chomp $line;
my ( $scaf, $pro_per ) = $line =~ m/\sHit=(.*?)\s.*?Percent_id=(.*?)$/g;
push @{$hash{$1}}, $2;
}

print Dumper (\%hash);


Output:
$VAR1 = {
          'scaffold293_size341291' => [
                                        '228.36676217765',
                                        '241.818181818182',
                                        '240',
                                        '233.076923076923',
                                        '241.904761904762',
                                        '227.461139896373',
                                        '222.666666666667'
                                      ],
          'scaffold4_size6989527' => [
                                       '235.023041474654',
                                       '247.663551401869',
                                       '247.663551401869',
                                       '224.137931034483',
                                       '236.734693877551',
                                       '237.634408602151',
                                       '237.777777777778',
                                       '231.707317073171',
                                       '230.337078651685'
                                     ]
        };



__DATA__
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=349 
Percent_id=228.36676217765
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=110 
Percent_id=241.818181818182
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=110 
Percent_id=240
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=130 
Percent_id=233.076923076923
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=105 
Percent_id=241.904761904762
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=193 
Percent_id=227.461139896373
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=150 
Percent_id=222.666666666667
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=217 
Percent_id=235.023041474654
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=107 
Percent_id=247.663551401869
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=107 
Percent_id=247.663551401869
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=174 
Percent_id=224.137931034483
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=98 
Percent_id=236.734693877551
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=93 
Percent_id=237.634408602151
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=90 
Percent_id=237.777777777778
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=82 
Percent_id=231.707317073171
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=89 
Percent_id=230.337078651685

On Sun, Sep 20, 2015 at 5:56 PM, Alaba, Oluwafemi (IITA) 
<o.al...@cgiar.org<mailto:o.al...@cgiar.org>> wrote:
Dear ALL,

I have a file that looks like this.

Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=349 
Percent_id=228.36676217765
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=110 
Percent_id=241.818181818182
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=110 
Percent_id=240
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=130 
Percent_id=233.076923076923
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=105 
Percent_id=241.904761904762
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=193 
Percent_id=227.461139896373
Query=sp|P59287|CASS_RICCO Hit=scaffold293_size341291 Bit=152 Length=150 
Percent_id=222.666666666667
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=217 
Percent_id=235.023041474654
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=107 
Percent_id=247.663551401869
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=107 
Percent_id=247.663551401869
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=174 
Percent_id=224.137931034483
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=98 
Percent_id=236.734693877551
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=93 
Percent_id=237.634408602151
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=90 
Percent_id=237.777777777778
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=82 
Percent_id=231.707317073171
Query=sp|P59287|CASS_RICCO Hit=scaffold4_size6989527 Bit=150 Length=89 
Percent_id=230.337078651685

I need hints to write a script that will recognise the fragments of protein in 
the same scaffolds.

Best wishes,

Alaba