Re: [Samtools-help] putting SNPs(the ambiguity codes) back into FASTA file?

[Joseph F. <jos...@gm...>]

Hi Hersh, Arthur, Heng (questions for you below),

If you compile as Heng specified, there should be a binary "seqtk" in the
same directory (as you show, Arthur). It'll be executable, but since it's
not (probably) on your path, you will need to type "./seqtk", e.g., which
will give you all the subcommands (similar to the usage of Heng's other
tools). So:

$ ./seqtk

Usage:   seqtk <command> <arguments>

Command: comp      get the nucleotide composite of FASTA/Q
         hety      regional heterozygosity
         fq2fa     convert FASTQ to FASTA
         subseq    extract subsequences from FASTA/Q
         maskseq   mask sequences
         mutfa     point mutate FASTA at specified positions
         mergefa   merge two FASTA/Q files

$ ./seqtk mutfa

Usage: seqtk mutfa <in.fa> <in.snp>

Note: <in.snp> contains at least four columns per line which are:
      'chr  1-based-pos  any  base-changed-to'.

Heng, I could probably experiment and find out, but will mutfa work for
insertions? deletions? I'm assuming that you could feed selected pileup
lines to mutfa, and the first four lines will satisfy mutfa's requirements,
yes? Also, I swear I remember a perl script "pileup2fq.pl" in a previous
release of something you wrote or were involved in (maq, bwa, or samtools)
... but I can't find anything like that. Is my sanity at risk?

Thanks,
~Joe







On Wed, Dec 22, 2010 at 3:20 AM, Hersh Parikh <her...@gm...> wrote:

> Agree. Documentation  on this will help a lot..
>
> Regards
> Hersh
>
>
>
> On 8 December 2010 17:19, Arthur Pastuer <art...@gm...> wrote:
>
>> Does anyone know how to use the tools that Heng attached to this e-mail? I
>> compiled with the command(not sure if that worked) that Heng mentioned, but
>> have not been able to actually use the tools. I have these files in my
>> directory: khash.h        kseq.h        seqtk        seqtk.c
>> seqtk.dSYM
>>
>> Art
>>
>> On Mon, Dec 6, 2010 at 3:54 PM, Heng Li <lh...@sa...> wrote:
>>
>>>  I have a utility for such a purpose. Source codes are attached. To
>>> compile:
>>>
>>> gcc -g -O2 seqtk.c -lz -o seqtk
>>>
>>> You may use "mutfa". In addition to this command, seqtk does a few other
>>> things including masking sequences, getting base composition, converting
>>> fastq to fasta and extracting subsequences. It is my small toolkit for
>>> processing fasta/q files.
>>>
>>> Heng
>>>
>>>
>>>
>>>
>>> --
>>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>>  Limited, a charity registered in England with number 1021457 and a
>>>  company registered in England with number 2742969, whose registered
>>>  office is 215 Euston Road, London, NW1 2BE.
>>>
>>>
>>>
>>>
>>> On Dec 6, 2010, at 12:13 PM, Arthur Pastuer wrote:
>>>
>>> > Is there a samtools feature that will allow you to process your FASTA
>>> file by putting SNPs (the ambiguity codes) back into the reference sequence
>>> that you used when calling SNPs? Any help would me much appreciated.
>>> >
>>> > Thanks, Art
>>> >
>>> ------------------------------------------------------------------------------
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>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
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-- 
Joseph Fass
Bioinformatics Programmer
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
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