Hello everyone,

I am a Perl newbie, and joined Perl Monks recently. This is my first post.

I am trying to parse a flat file using Perl and I have to modify a few things in it. Here is a part of my input file:

>sequence1 123.3
ATGACGTAGACGATGAGTAGACGATAGCAGTGACAGGTGAGTG\n
ATGACGATGAGTAGAGACGGGGGTAGAGGGGGATAGATAGAGANNNNNNNN\n
ATAGACAGATAANNNNNNNNNNNNNNNNNAGATGAGACAGATANNNNNNN
>sequence2 143.5
ATGCGATGCNNNNNNCGTAGCTGANNNNNNCGATGCTGATGCTC\n
CGTAGTCTGCTAGCTAGTCNNNNNNCGTAGTCGATCGATCGANNNNNNCGTGCATGC\n
CGATGCTACGGATNNNNNCGATCGATCGATCGACNNNNNCGATCAGCTAG\n
CCCCGCTAGTCANNNNN
>sequence3 132.3
ATGCTGATCAGCTACGCTAGCNNNNNCGATCGATCGATCGACTAGCNNNNNNCGATCCGAGCT\n
CGATCGATCGATCGATCGANNNNNCGATCGATCGACTAGCNNNNNCGATCGATCGA\n
CGATCGATCGA
>C1132423 123.4
ATCGTGCATGCATCGATCGACTACGCTGCTACGATCGACTGCTAGCTACGCTAC\n
CGTCGATCGATCGACTACGCTGACTGACTAGCTAG
>C1123234 176.4
GCTAGCGATCGCACCGATCGATCGTACGCTACGATCGATCGATCGATCGACTGT\n
CGATCGATCGATCGATCGATCGA
>C1123546 531.1
CGTAGCTACGATCGATCGATCGACTAGCTACGATCGATCGACTAGCTAGCTAGCTAG

Note: '/n' = sequences are separated with new line.

I am modifying this file(both header & sequence data).
The example output for this file should be :

>count1.1
ATGACGTAGACGATGAGTAGACGATAGCAGTGACAGGTGAGTGATGACGATGAGTAGAGACGGGGGTAGAGGGGGATAGATAGAGA
>count1.2
ATAGACAGATAA
>count1.3
AGATGAGACAGATA
>count2.1
ATGCGATGC
>count2.2
CGTAGCTGA
>count2.3
CGATGCTGATGCTCCGTAGTCTGCTAGCTAGTC
>count2.4
CGTAGTCGATCGATCGA
>count2.5
CGTGCATGCCGATGCTACGGAT
>count2.6
CGATCGATCGATCGACCGATCAGCTAGCCCCGCTAGTCA
>count3.1
ATGCTGATCAGCTACGCTAGC
>count3.2
CGATCGATCGATCGACTAGC
>count3.3
CGATCCGAGCTCGATCGATCGATCGATCGA
>count3.4
CGATCGATCGACTAGC
>count3.5
CGATCGATCGACGATCGATCGA
>count4.1
ATCGTGCATGCATCGATCGACTACGCTGCTACGATCGACTGCTAGCTACGCTACCGTCGATCGATCGACTACGCTGACTGACTAGCTAG
>count5.1
GCTAGCGATCGCACCGATCGATCGTACGCTACGATCGATCGATCGATCGACTGTCGATCGATCGATCGATCGATCGA
>count6.1
CGTAGCTACGATCGATCGATCGACTAGCTACGATCGATCGACTAGCTAGCTAGCTAG

Can someone please help me with this?
I would really appreciate it!!!

Thanks in advance.

In reply to Parsing and Modifying a flat file in perl by ad23

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