Exemplo n.º 1
0
#!/usr/bin/python
#from BioSQL import BioSeqDatabase
#import MySQLdb as mdb
from seqdbutils import gi2taxid,taxid2name,genInfo2fasta,getparenttaxid,blast2fasta,taxid2rank,taxid2cladename,blast2superkingdom,browsetaxonomy

from Bio import AlignIO
from seqdbutils import filterFastaColumnsByFirstSeq
#alignment = AlignIO.read("5BhitsculledbygenusUnder80clustalo.fst", "fasta")
#print _findFastaPosWOdashes(alignment[0].seq,626)
#print alignment[:20,2342:2352]
#print alignment[:20,2342:2984]

filterFastaColumnsByFirstSeq("5BhitsculledbygenusUnder80clustalo.fst","5BhitsculledbygenusUnder80627-1220.fst",627,1221)
#filterFastaColumnsByFirstSeq("5BhitsculledbygenusUnder80clustalo.fst","5BhitsculledbygenusUnder80clustalo951-1085.fst",951,1085)


#server = BioSeqDatabase.open_database(driver="MySQLdb", user="******",
#                     passwd = "", host = "localhost", db="bioinfo")

#gilist = [84043963,355751524,355565935,387763418,114579120,73969383,40788346,
#          332251518,5002645,301769165,410352203,168267520]

#taxidlist = [gi2taxid(x) for x in gilist]
#print taxidlist

#namelist = [taxid2name(x) for x in taxidlist]
#print namelist

#parentlist = [taxid2name(getparenttaxid(getparenttaxid(getparenttaxid(getparenttaxid(x))))) for x in taxidlist]
#print parentlist
Exemplo n.º 2
0
#!/usr/bin/python

from seqdbutils import filterFastaColumnsByFirstSeq

infile = "5BhitsculledbygenusUnder80linsi-trimmed.fasta"
outfile = "5BhitsculledbygenusUnder80linsi-trimmed-tailless.fasta"
StartResidue = 627 #First sequence
EndResidue = 1221 #First sequence
filterFastaColumnsByFirstSeq(infile,outfile,StartResidue,EndResidue)
Exemplo n.º 3
0
#!/usr/bin/python
from Bio import AlignIO
from seqdbutils import filterFastaColumnsByFirstSeq
#alignment = AlignIO.read("5BhitsculledbygenusUnder80clustalo.fst", "fasta")
#print _findFastaPosWOdashes(alignment[0].seq,626)
#print alignment[:20,2342:2352]
#print alignment[:20,2342:2984]

filterFastaColumnsByFirstSeq("5BhitsculledbygenusUnder80clustalo.fst","5BhitsculledbygenusUnder80clustalo627-1220.fst",627,1220)
filterFastaColumnsByFirstSeq("5BhitsculledbygenusUnder80clustalo.fst","5BhitsculledbygenusUnder80clustalo951-1085.fst",951,1085)