sffinfo -s inputfile

[Xterra]

sklages

I am trying to combine sffinfo with a code that can get rid of the extra information in the ID line and at the same time remove the new line at the end of each line. Originally, I was hoping there was an option in sffinfo that could do exactly what I needed. Not being an scripter makes the task of finding the right code a little more challenging.

Write a little perl script to remove the newline at the end of the sequence lines.

Not Perl but AWK:

awk '/^>/ {
print (buff ? buff RS : null) $0
buff = null; next
}
{
buff = buff ? buff FS $0 : $0
}
END { print buff }' infile

[sklages]

look at your previous post and see what you have requested.

Write a little perl script to remove the newline at the end of the sequence lines.

[Xterra]

Very nice!

However, I still have a problem, the file now look like this (60 characters per line):

>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG
CCCCGGGG

And I need something like this (the entire sequence in one line):

>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCCCGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGG

Thanks in advance!

[sklages]

Is there any way to chage the 'format' of the output fasta file generated by sffinfo -s?
Using the following code

sffinfo -s Inputfile.sff > Outputfile.fna

sffinfo -s Inputfile.sff  | perl -lpe 's/^(\>\S+).+/$1/'  > Outputfile.fna

should work in most cases :-)

[Xterra]

Is there any way to chage the 'format' of the output fasta file generated by sffinfo -s?
Using the following code

sffinfo -s Inputfile.sff > Outputfile.fna

This is what I get

>GHXCZCC01AJ8CJ length=314 xy=0113_1201 region=1 run=R_2010_05_27_13_55_50_
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGGCGA
AGAGGCTGGTCAGCGCACGGGTGTCCCTGCCCGCCGTCTGCCCCACCGTACGGGTGCTCC
CGTCAACGCCGGCAAAGAGTAGCATCACAATCAAGACCTTAGCCCAGTTCCCCACCATGG
AATAGTAGGCAAGGCCCGCCAGGACTCCCCAGTGGACCCCCGCCACCATATCTACGACAG
CTTGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCA
TCATATCCACGCAC
>GHXCZCC01APUO5 length=312 xy=0177_1303 region=1 run=R_2010_05_27_13_55_50_
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCCCGGGGCGAAG
AGGCTGGTCAGCGCACGGGTGTCCCTGCCCGCCGTCTGCCCCACCGTACGGGTGCTCCCG
TCAACGCCGGCAAAGAGTAGCATCACAATCAAGACCTTAGCCCAGTTCCCCACCATGGAA
TAGTAGGCAAGGCCCGCCAGGACTCCCCAGTGGGCCCCCGCCACCATATCCACGACAGCT
TGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCATC
ATATCCACGCAC
>GHXCZCC01AQSRP length=314 xy=0188_0403 region=1 run=R_2010_05_27_13_55_50_
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGGTG
AAGAGGCTGGTCAGCGCACGGGTGTTCATACCCGCCGTCTCCCCACCGTACGGGTGCTCC
CGTCAACGCCGGCAAAGAGTAGCATCGCAATCAAGACCTTAGCCCAGTTCCCCACCATGG
AATAGTAGGCAAGGCCCGCCAGGACTCCCCAGTGGGCCCCCGCCACCATATCCACGACAG
CTTGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCA
TCATATCCACGCAC

Would it be possible to change it to

>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGGCGAAGAGGCTGGTCAGCGCACGGGTGTCCCTGCCCGCCGTCTG CCCCACCGTACGGGTGCTCCCGTCAACGCCGGCAAAGAGTAGCATCACAATCAAGACCTTAGCCCAGTTCCCCACCATGGAATAGTAGGCAAGGCCCGCC AGGACTCCCCAGTGGACCCCCGCCACCATATCTACGACAGCTTGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCA TCATATCCACGCAC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCCCGGGGCGAAGAGGCTGGTCAGCGCACGGGTGTCCCTGCCCGCCGTCTGCC CCACCGTACGGGTGCTCCCGTCAACGCCGGCAAAGAGTAGCATCACAATCAAGACCTTAGCCCAGTTCCCCACCATGGAATAGTAGGCAAGGCCCGCCAG GACTCCCCAGTGGGCCCCCGCCACCATATCCACGACAGCTTGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCATC ATATCCACGCAC
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGCCCCGGGGTGAAGAGGCTGGTCAGCGCACGGGTGTTCATACCCGCCGTCT CCCCACCGTACGGGTGCTCCCGTCAACGCCGGCAAAGAGTAGCATCGCAATCAAGACCTTAGCCCAGTTCCCCACCATGGAATAGTAGGCAAGGCCCGCC AGGACTCCCCAGTGGGCCCCCGCCACCATATCCACGACAGCTTGTGGGATCCGGAGTAACTGCGATACCACCAGGGCCGTTGTAGGTGACCAGTTCATCA TCATATCCACGCAC

Any help will be greatly appeciated!