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Parsing and masking regions from a single fasta file with subsequence

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Top Forums Shell Programming and Scripting Parsing and masking regions from a single fasta file with subsequence
# 1  
Old 09-25-2014
Parsing and masking regions from a single fasta file with subsequence
HI,

I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
Code:
4353..5633
6795..9354
1034..14456

I want a script which can mask these region in a single complete genome fasta file with the alphabet N

kindly help
Last edited by Don Cragun; 09-25-2014 at 06:51 AM.. Reason: Add CODE tags.
# 2  
Old 09-25-2014
You have given some sample input, can you please provide your expected output?

Also please advise what you have tried so far?
# 3  
Old 09-25-2014
The content in the file

Code:
>CP008559 Pseudomonas aeruginosa SRS4, complete genome
tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat
gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc
tcttgggacggcgcttttctgtgcataactcgacgaagcccagcaactgcgtgtttctcc
ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg
gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta
cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc
ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtacggc
ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat
ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc
aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg
tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc
tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca
gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc
cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtgg
tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgacccctacg
agccggaagagcccagcatcgatccgctggccgccgccatgccggccggagccgcacctg
cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca
accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg
ccgcctggcaggtggcggacaacctcaagcacggttacaacccgctgttcctctacggtg
gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga
acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg
ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt
tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca
ccttcaatgccctcctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga
aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg
ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggctgagcagg
cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg
tgcgcgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc
cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc
tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg
atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc
tctccaaggagctgaccaaccacagcctgccggagatcggcgtagccttcggcggtcggg
atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg
atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag
gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa
ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg
gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaggtcgagctggttggt
cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg
atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag
aaactcctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat

I want the out the out output as:


Code:
>CP008559 Pseudomonas aeruginosa SRS4, complete genome.
tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat
gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc
tcttgggacggcgcttttctgtgcataactcgacgaagcccagcaactgcgtgtttctcc
ggcaggcaaaagNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgaagccgaaggcgacgaattgcgtg
tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc
tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca
gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc
cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtgg
tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgacccctacg
agccggaagagcccagcatcgatccgctggccgccgccatNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNtgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccacaccttcaatgccctcctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccgaaggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtggccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggctgagcaggcgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg
tgcgcgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc
cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc
tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg
atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc
tctccaaggagctgaccaaccacagcctgccggagatcggcgtagccttcggcggtcggg
atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg
atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag
gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa
ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg
gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaggtcgagctggttggt
cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg
atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag
aaactcctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat


The N should be based on the list of subranges given as:
Code:
188..250
375..550
etc...

Last edited by Don Cragun; 09-25-2014 at 06:54 AM.. Reason: Add CODE tags.
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