I'm writing a script that takes two command line options, a file containing
barcodes and a file containing sequences. I've managed to create output files
for each barcode with the matching and corresponding sequences in it.
For the next part of my script, I'm trying to create more output files by using
the output files creating earlier as input files. So my first output files
contains sequences in a simple format. Now each needs to be converted to fasta,
then used mafft and quicktree commands on them.
However, this part only converts one of the original output files into fasta,
running mafft and quicktree on that one.
#!/usr/bin/python
import sys
import os
fname = sys.argv[2]
barcodefname = sys.argv[1]
barcodefile = open(barcodefname, "r")
for barcode in barcodefile:
barcode = barcode.strip()
print "barcode: %s" % barcode
infname = "%s.%s" % (fname,barcode)
inf = open(infname, "w")
handle1 = open(fname, "r")
for lines in handle1:
seqid = lines[0:3]
i = 4
potential_barcode = lines[i:(i+len(barcode))]
if potential_barcode == barcode:
outseq = lines[i+len(barcode):]
sys.stdout.write(outseq)
inf.write("%s %s%s" % (seqid,barcode,outseq))
handle1.close()
inf.close()
barcodefile.close()
infname = "%s.%s" %(fname,barcode)
fastafname = infname + ".fasta"
mafftfname = fastafname + ".mafft"
stfname = infname + ".stock"
# convert simple to fasta #
for file in infname
handle = open(infname, "r")
outf = open(fastafname, "w")
for line in handle:
linearr = line.split()
seqids = linearr[0]
seq = linearr[1]
outf.write(">%s\n%s\n" % (seqids,seq))
handle.close()
outf.close()
# align using mafft #
cmd = "mafft %s > %s" % (fastafname,mafftfname)
sys.stderr.write("command: %s\n" % cmd)
os.system(cmd)
sys.stderr.write("command done\n")
#convert fasta alignment to stockholm
# fasta_to_stockholm seq.data.txt.fasta.mafft > TEST.stockholm
cmd = "fasta_to_stockholm %s > %s" % (mafftfname, stfname)
sys.stderr.write("command: %s\n" % cmd)
os.system(cmd)
sys.stderr.write("command done\n")
#run quicktree to get distance matrix
# quicktree -out m TEST.stockholm
cmd = "quicktree -out m %s" % stfname
sys.stderr.write("Command: %s\n" % cmd)
os.system(cmd)
sys.stderr.write("command done\n")
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