Hello everybody
I am trying to find a ready Perl scrip, or any equivalent solution, to help me my data analysis task.
I need a code that takes a CVS file contains DNA ranges, and extract them from two reference sequences, then append them, and write them to a fasta file.
For example:
DNA ref. Sequence 1:
AAAAAGGGGG
DNA ref. Sequence 2:
CCCCCTTTTTT
The CVS file contains five columns, the first is the name of that particular range, next two columns define the range from the first sequence, i.e. where to start extraction and where to end it, and the last two describe the-the range from the second sequence, for example:
seq1 1 5 5 10
seq2 5 10 1 5
seq3 1 6 4 10
The Perl script output will be
>seq1
AAAAATTTTT
>seq2
GGGGGCCCCC
>seq3
AAAAAGCCTTTTTT
The only similar tool I found is the DNA range extractor, part of Sequence Manipulation Suite. However, it can extract only one range per time per sequence, which makes it unsuitable for extracting hundreds of ranges.
Many thanks
Fadi
I am trying to find a ready Perl scrip, or any equivalent solution, to help me my data analysis task.
I need a code that takes a CVS file contains DNA ranges, and extract them from two reference sequences, then append them, and write them to a fasta file.
For example:
DNA ref. Sequence 1:
AAAAAGGGGG
DNA ref. Sequence 2:
CCCCCTTTTTT
The CVS file contains five columns, the first is the name of that particular range, next two columns define the range from the first sequence, i.e. where to start extraction and where to end it, and the last two describe the-the range from the second sequence, for example:
seq1 1 5 5 10
seq2 5 10 1 5
seq3 1 6 4 10
The Perl script output will be
>seq1
AAAAATTTTT
>seq2
GGGGGCCCCC
>seq3
AAAAAGCCTTTTTT
The only similar tool I found is the DNA range extractor, part of Sequence Manipulation Suite. However, it can extract only one range per time per sequence, which makes it unsuitable for extracting hundreds of ranges.
Many thanks
Fadi
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