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src/c/o/cogent-1.5.3/cogent/app/blast.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath, \
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
    return (not line) or line.isspace() or line.startswith('[')
 
FastaCmdFinder = LabeledRecordFinder(is_fasta_label, ignore=fastacmd_is_crap)
 
def seqs_from_fastacmd(acc_list, blast_db,is_protein=True):
    """Get dict of description:seq from fastacmd."""
    fasta_cmd_res = fasta_cmd_get_seqs(acc_list, blast_db=blast_db, \
        is_protein=is_protein)
    recs = FastaCmdFinder(fasta_cmd_res['StdOut'])
                app.Parameters['-d'].Value)['StdOut']
            seqs_to_check = []
            for s in FastaCmdFinder(fasta_cmd_get_seqs(\
                unchecked_ids.keys(), app.Parameters['-d'].Value)['StdOut']):
                seqs_to_check.extend(s)

src/p/y/pycogent-HEAD/cogent/app/blast.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath, \
    get_tmp_filename, guess_input_handler, ApplicationNotFoundError
from cogent.parse.fasta import FastaFinder, LabeledRecordFinder, is_fasta_label
from cogent.parse.blast import LastProteinIds9, QMEBlast9, QMEPsiBlast9, BlastResult
from cogent.util.misc import app_path
    return (not line) or line.isspace() or line.startswith('[')
 
FastaCmdFinder = LabeledRecordFinder(is_fasta_label, ignore=fastacmd_is_crap)
 
def seqs_from_fastacmd(acc_list, blast_db,is_protein=True):
    """Get dict of description:seq from fastacmd."""
    fasta_cmd_res = fasta_cmd_get_seqs(acc_list, blast_db=blast_db, \
        is_protein=is_protein)
    recs = FastaCmdFinder(fasta_cmd_res['StdOut'])
                app.Parameters['-d'].Value)['StdOut']
            seqs_to_check = []
            for s in FastaCmdFinder(fasta_cmd_get_seqs(\
                unchecked_ids.keys(), app.Parameters['-d'].Value)['StdOut']):
                seqs_to_check.extend(s)