Parsing and extracting from text file (FASTA format)
Hi,
This question is from a specialised field but guess could be solved by any expert in Perl programing.
I have an genome file in a FASTA format (text) and a file with some coordinates (i.e positions giving the start and end position) in an excel file. Given the coordinates I would like to extract the sequence information from the FASTA file (text file) and then additionally also calculate the number of A's, G's, T's and C's in the sequence extracted in a seperate file (csv file)
For example the FASTA file looks like this
>gi|12222253|gb|AL438840.1
CGGTTTTAACAGTTAACAGGCAAGTT
GACAATCTCTGAGTTACGTTCTATAA
AATTTTCTTTTTCACGCTTAGCACAG
AAGATAAAAGAAGATGACAAGCACAC
GCGTTTTCGAGTAAAGAAACATTTCC
TCCAGATCCAAAGATGGTGTTCTAAA
AGCCGATAAGGTTGACTTGGCGATAG
GAAATATTTAAAGATTGTATTGATAC
ACGATGGATGTGGTGATGTATGGCAG
CACATTTCCTCTAGCACCATCTGACG
ATCTTGAAATTTGTGATACTAGTAAT
TGTCACAAGTCCCACCAAATCATTCA
CGTATGTGTGAAAGTTATTACCAATG
TCAGTTCTAGCAAGAAGAAAACCCCA
AATACAAAATTACAGTCAAATTATCA
TCTTGAGARTTTCTATTTAAAGATTG
TTGCTGAAAACGATGGATGTGGTGAT
GTTTCAAAGCACATTTCCTCTAGCAC
ATCTTGAAATTTGTGATACTAGTAAT
TGTCACAAGTCCCACCAAATCATTCA
CGTATGTGTGAAAGTTATTACCAATG
TCAGTTCTAGCAAGAAGAAAACCCCA
AATACAAAATTACAGTCAAATTATCA
TCTTGAGARTTTC
In the fasta file the attributes following > doesnt matter and the position starts from the
CGGTTTTA
where C is position 1, G is position 2, G is position 3, T is position 4, T is position 5 and so on..
The output of the file should be like this (output1)
>MID1, Chr1, +strand, position 10-20, length 10
CAGTTAACAG
>MID2 chr2, +strand, position 30-35 length 5
CAACC
Output2 -No of AGCT
A G C T
MID1 4 2 2 2
MID2 2 0 3 0
Can someone point me to a resource where I can do this automatically, like if there is any software or program already available or could some expert help solve this in perl.
Thank you
markposition.xls
This question is from a specialised field but guess could be solved by any expert in Perl programing.
I have an genome file in a FASTA format (text) and a file with some coordinates (i.e positions giving the start and end position) in an excel file. Given the coordinates I would like to extract the sequence information from the FASTA file (text file) and then additionally also calculate the number of A's, G's, T's and C's in the sequence extracted in a seperate file (csv file)
For example the FASTA file looks like this
>gi|12222253|gb|AL438840.1
CGGTTTTAACAGTTAACAGGCAAGTT
GACAATCTCTGAGTTACGTTCTATAA
AATTTTCTTTTTCACGCTTAGCACAG
AAGATAAAAGAAGATGACAAGCACAC
GCGTTTTCGAGTAAAGAAACATTTCC
TCCAGATCCAAAGATGGTGTTCTAAA
AGCCGATAAGGTTGACTTGGCGATAG
GAAATATTTAAAGATTGTATTGATAC
ACGATGGATGTGGTGATGTATGGCAG
CACATTTCCTCTAGCACCATCTGACG
ATCTTGAAATTTGTGATACTAGTAAT
TGTCACAAGTCCCACCAAATCATTCA
CGTATGTGTGAAAGTTATTACCAATG
TCAGTTCTAGCAAGAAGAAAACCCCA
AATACAAAATTACAGTCAAATTATCA
TCTTGAGARTTTCTATTTAAAGATTG
TTGCTGAAAACGATGGATGTGGTGAT
GTTTCAAAGCACATTTCCTCTAGCAC
ATCTTGAAATTTGTGATACTAGTAAT
TGTCACAAGTCCCACCAAATCATTCA
CGTATGTGTGAAAGTTATTACCAATG
TCAGTTCTAGCAAGAAGAAAACCCCA
AATACAAAATTACAGTCAAATTATCA
TCTTGAGARTTTC
In the fasta file the attributes following > doesnt matter and the position starts from the
CGGTTTTA
where C is position 1, G is position 2, G is position 3, T is position 4, T is position 5 and so on..
The output of the file should be like this (output1)
>MID1, Chr1, +strand, position 10-20, length 10
CAGTTAACAG
>MID2 chr2, +strand, position 30-35 length 5
CAACC
Output2 -No of AGCT
A G C T
MID1 4 2 2 2
MID2 2 0 3 0
Can someone point me to a resource where I can do this automatically, like if there is any software or program already available or could some expert help solve this in perl.
Thank you
markposition.xls
You will need Perl module Spreadsheet::ParseExcel (if on unix) or Win32::OLE (if on windows) to parse Excel spreadsheet using Perl. The code in Perl would be simple. Let me know which OS platform you are running it on.
ASKER
Hi, I have these perl modules, but if the excel sheet is converted to CSV format too I am okay with it. I am having Windows Vista.
Thanks for looking at it.
Thanks for looking at it.
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