#!/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
#!/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)
#!/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)