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Difference between revisions of "Get.seqs"

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(Algorithm)
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# read accnos file into a set<string> container, close the file
 
# read accnos file into a set<string> container, close the file
 
# read through the file to be parsed and for each entry, if the sequence name is in the set<string> container:
 
# 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
+
* spit the data out to the new file and delete the entry from the set<string> container
** otherwise do nothing
+
* otherwise do nothing

Revision as of 13:35, 8 July 2009

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.


Options

accnos, fasta, name, group, alignreport; each takes a file name


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
  • otherwise do nothing