def import_fasta(fastaFile):
seqDict = fol.blast_dict(fastaFile)
longList = fol.one_line_d(fastaFile).keys()
descDict = {}
lenDict = {}
for header in seqDict.keys():
lenDict[header] = len(seqDict[header])
for header in longList:
parts = header.rstrip("\n").lstrip(">").split(" ")
descDict[parts[0]] = " ".join(parts[1:])
return lenDict, descDict, seqDict
import Fasta_one_line as fol
infile = open("transposase_clusters.txt", 'r')
fasta = fol.blast_dict(
"/work/mpesesky/Plasmids/NCBI_Plasmids/taxonAnalysis/transposases.faa")
used_families = []
for line in infile:
nodes = line.rstrip().split("\t")
clusterName = nodes[0]
if clusterName in used_families:
print(clusterName)
exit()
outfileName = clusterName + ".faa"
outfile = open(outfileName, 'w')
for node in nodes[1:]:
if "|" not in node:
continue
if node.startswith("ref"):
nodeName = node
else:
nodeName = "ref|{}|".format(node.split("|")[1])
try:
seq = fasta[nodeName]
except KeyError:
print(nodeName)
exit()
outfile.write(">{}\n{}\n".format(nodeName, seq))