Off topic:Miranda Output Parsing

Question

[Patrick]

Hello everyone,

I am using miranda and would like to write a perl parser to extract the regions I am putting in Bold in what is following I hope you can guide me throught writing it :

here is the output (I only want to extract the bold tagged part that means that I have a match between my miRna and cDNA (output is trancated, the * TEXT * is supposed to be BOLD text Its not working inside code tags here)

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing Scan: 5102 vs ENST00000403423
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Score for this Scan:
No Hits Found above Threshold
Complete

Read Sequence:ENST00000356294 cdna:pseudogene chromosome:GRCh37:1:248246965:248247898:-1 gene:ENSG00000197067(930 nt)
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Performing Scan: 5102 vs ENST00000356294
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Score for this Scan:
No Hits Found above Threshold
Complete

Read Sequence:ENST00000431838 cdna:pseudogene chromosome:GRCh37:1:247996651:247997590:-1 gene:ENSG00000230576(940 nt)
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Performing Scan: **5102** vs **ENST00000431838**
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   Forward:    Score: 140.000000  Q:2 to 25  R:**393 to 418** Align Len (23) (56.52%) (69.57%)

   Query:    3' caGGCACGAACGGAUCGCUUGAGUGg 5'
                  || |||   : |: | |:||||| 
   Ref:      5' taCCCTGCAATTATGACCAGCTCACt 3'

   Energy:  **-16.430000 kCal/Mol**

Scores for this hit:
>5102    ENST00000431838    140.00    -16.43    2 25    393 418    23    56.52%    69.57%

Score for this Scan:
Seq1,Seq2,Tot Score,Tot Energy,Max Score,Max Energy,Strand,Len1,Len2,Positions
>>5102    ENST00000431838    140.00    -16.43    140.00    -16.43    28    26    940     393
Complete

Read Sequence:ENST00000438288 cdna:pseudogene chromosome:GRCh37:1:247830189:247831143:1 gene:ENSG00000230411(955 nt)
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Performing Scan: 5102 vs ENST00000438288
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Score for this Scan:
No Hits Found above Threshold
Complete

Read Sequence:ENST00000438881 cdna:known chromosome:GRCh37:17:4835625:4838274:1 gene:ENSG00000185245(2339 nt)
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Performing Scan: **5102** vs **ENST00000438881**
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

   Forward:    Score: 147.000000  Q:2 to 25  R:**615 to 641** Align Len (24) (66.67%) (70.83%)

   Query:    3' caGGCACGA-ACGGAUCGCUUGAGUGg 5'
                  || | ||   || || ||||||:| 
   Ref:      5' caCCCTTCTCCTCCAAGAGAACTCGCt 3'

   Energy:  **-20.080000 kCal/Mol**

Scores for this hit:
>5102    ENST00000438881    147.00    -20.08    2 25    615 641    24    66.67%    70.83%


   Forward:    Score: 143.000000  Q:4 to 25  R:444 to 471 Align Len (23) (73.91%) (82.61%)

   Query:    3' caGGCACGAAC--GGAUCGCUUGAGugg 5'
                  || ||| ||  |:|:||||||||   
   Ref:      5' tgCCCTGCGTGGTCTTGGCGAACTCcaa 3'

   Energy:  -28.320000 kCal/Mol

Scores for this hit:
>5102    ENST00000438881    143.00    -28.32    4 25    444 471    23    73.91%    82.61%

Score for this Scan:
Seq1,Seq2,Tot Score,Tot Energy,Max Score,Max Energy,Strand,Len1,Len2,Positions
>>5102    ENST00000438881    290.00    -48.40    147.00    -28.32    30    26    2339     615 444
Complete

Read Sequence:ENST00000329125 cdna:known chromosome:GRCh37:17:4835592:4838325:1 gene:ENSG00000185245(2501 nt)

Thank you

Pat