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Get.seqs

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Revision as of 17:32, 23 June 2009 by Pschloss (Talk | contribs)

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Given a list of accession numbers (i.e. sequence names) and one or more file formats, generate a new file that contains only those sequences. The keep option indicates that you want the file to contain the sequences; if keep=false, generate files without those sequence names.


Options

accnos, fasta, name, group, alignreport; each takes a file name and keep (default=true)


Required

accnos and one of fasta/name/group/alignreport


Output

*.pick.*


Algorithm

  1. read accnos file into a set<string> container, close the file
  2. read through the file to be parsed and for each entry, if the sequence name is in the set<string> container:
    • spit the data out to the new file and delete the entry from the set<string> container (the opposite is true when keep=false)
    • otherwise do nothing