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Convert XML file to FASTA

Hi everyone,

I have downloaded polypeptide data which format is called Chado XML. As I opened it, it seems quite a new format in comparison to other formats, so I would like to know if there's any way to convert to FASTA, as it is the format needed as input.

I really appreciate any help you can provide.

chado-xml conversion flybase polypeptides
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Tye Kahn • Tye Kahn

According to this wiki page, there's a way to convert TO Chado XML using bioperl, maybe it can be used the other way around as well?

BioPerl has a write-adapter for Chado-XML, Bio::SeqIO::chadoxml. This means that any file format which Bioperl can pass can be exported to Chado-XML.

If you are not familiar with the bioperl SeqIO system, you can do it on the command line, like this:

bp_seqconvert --from genbank --to chadoxml < NT_021877.gbk

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written by jonasmst jonasmst

Yes, unfortunately, it seems that it only works the other way around, obtaining XML files instead of getting rid of them.

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written by Tye Kahn • Tye Kahn

1 answer

write a SAX or Stax parser to extract the data

        <name>CG9570-PA</name>
        <timelastmodified>2004-06-05 04:27:57</timelastmodified>
        <residues>MTCTLVLLIASVLHFRMRGSCLLDIERFPVIPGTIYAGHIAYCAILYFLHDLEILPTRYRSRMGWLTTFLIELVLGVAFMEVLALWLW
CSVEHILHLSTQFVLRRYLGVSTEVYQRWEWAIMGGLMTTLAAMLWINAFEATETTKAERVSKDVKDIRMKAVLCQREEKQKQDHDLEKIEQPAPEPEESQNPDEVQLPENHLK
LLATTTDC</residues>
        <is_obsolete>0</is_obsolete>
        <uniquename>FBpp0070001</uniquename>
        <seqlen>210</seqlen>
        <md5checksum>54d605138ac28e802cdf493751b71b17</md5checksum>
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for your early answer. Are these parsers usually written in java? My programming languages only comprise Perl, Python, R, bash and MySQL. Even so, I'll see if I can work on it.

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written by Tye Kahn • Tye Kahn

In the end I found a site in the same database where the data is included in the desired format, so I didn't need to perform it. Anyway, thanks for your help.

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written by Tye Kahn • Tye Kahn

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