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Question: Converting Ab1 Trace Files Into Scf Trace Files
3
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I've got a large collection of trace sequence files which are in .ab1 file format. I need to import the TRACE DATA (not just the base-calls) into Matlab. Matlab has an scf reader so I though it would be easy to find a little tool that could convert ab1 files to scf files, but alas.

  • I've tried SeqVerter (doesn't output in trace format only base-calls)
  • DNA Baser (doesn't install)
  • Staden (can't get to install)
  • Tried abiparser.py (error in file format)

Any suggestions, Thanks Will

ADD COMMENTlink 9.9 years ago Will 4.5k • updated 17 months ago BioApps • 740
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0

re Staden: which version of Staden and which platform?

ADD REPLYlink 9.9 years ago
Darked89
4.2k
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What was your problem with staden ?

ADD REPLYlink 9.9 years ago
Pierre Lindenbaum
120k
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0

What OS are you using/have access to ? That would help answer the question.

ADD REPLYlink 9.9 years ago
Jan Van Haarst
• 300
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4 programs and none works? There must be something wrong with your computer :)

ADD REPLYlink 17 months ago
BioApps
• 740
7
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This works for me (5 minutes ago on OSX) :

./convert_trace -out_format scf < trace.ab1 > trace.scf

After conversion I viewed both in a trace viewer(FinchTV), and they looked the same.

ADD COMMENTlink 9.9 years ago Jan Van Haarst • 300
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0

this is what I ended up doing ... I didn't notice until later that you can install just the "conversion" utilities. It was all of the graphics stuff that was having trouble compiling in the end.

ADD REPLYlink 9.9 years ago
Will
4.5k
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0

this suggestion worked well for me. the bioperl solution didn't work out of the box for me, and whatever I did to "fix" it just resulted in the called base's trace showing up at a particular peak position (no secondary info). In any case, convert_trace does. This should be able to process directory-wide matching a wildcard/pattern

#!/bin/bash
#ab1toscf.bash
shopt -s extglob
while test $# -gt 0
do
    fn="$1"
    bn="$(basename $fn)"
    dn="$(dirname $fn)"
    bc="${bn%.*}"
    fe=".${bn##*.}"
    oe=".scf"
    out="${dn}/${bc}${oe}"
    `convert_trace -out_format scf &lt;$fn &gt;$out`
    shift
done
ADD REPLYlink 7.0 years ago
pagel
• 90
• updated 17 months ago
RamRS
21k
4
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A bioperl solution extremely simple for a multi seq abi file, tested in every OS you can imagine:

use Bio::SeqIO;

$in = shift or die;
$out = shift or die;

$seq_in = Bio::SeqIO->new('-file' => "<$in", '-format' => "abi");
$seq_out = Bio::SeqIO->new('-file' => ">$out", '-format' => "scf");

while ($seq = $seq_in->next_seq) {
    $seq_out->write_seq($seq);
}

Of course, it's bioperl. So, check the consistency of your result.

ADD COMMENTlink 9.9 years ago Jarretinha 3.3k • updated 17 months ago RamRS 21k
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0

wow now that's a simple solution - hat is off to BioPerl

ADD REPLYlink 9.9 years ago
Istvan Albert
80k
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0

Under the hood, it uses Staden's io_lib, so you'll have to get that installed anyway.

ADD REPLYlink 9.9 years ago
Jonathan Manning
• 620
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That's absolutely right. bioperl-ext has a bunch of libs collected from other applications. And that's why it can handle such a large collection of file formats.

ADD REPLYlink 9.9 years ago
Jarretinha
3.3k
2
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I think Bioperl should have this functionality. The Bio::SeqIO documentation states it can handle both ABI/AB1 and SCF trace file formats.

Also, if you have access to an ABI Sequencer, the current version of the Data Collection software can be made to write .scf files in addition to .ab1 files. And if you ever wish to do anything really funky with ABI raw files, ABI provides the full specification for the ABIF file format here.

ADD COMMENTlink 9.9 years ago Phis ♦ 1.0k
1
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The converter supplied in the package Staden works perfectly for such tasks. For example, from within your folder containing the .ab1 files, you can run:

for i in $(ls *.ab1); do convert_trace -out_format scf < $i > ${i%.ab1*}.scf; done
ADD COMMENTlink 4.5 years ago Michael Gruenstaeudl • 40 • updated 17 months ago RamRS 21k
0
Entering edit mode

DNA Baser Assembler can convert between several formats including ABI to SCF.
If it doesn't install you have some kind of overzealous antivirus overreacting.

Here is a RAR package that you DON'T have to install: http://www.dnabaser.com/download/Biology-tools-package.rar
Just extract the files BEFORE you execute them.

Another program that will automatically convert ALL you ABI files to SCF is [Chromatogram Explorer][2].

ADD COMMENTlink 17 months ago BioApps • 740

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