gistfile1.py

	# this one works, plink is in cwd + conversion to BED files works flawlessly
	
for f in usable_files:
	# gid is the genotype-ID
	gid = f.split("/")[-1].split("_")[1].replace("file","")
	# converts the genotyping file to plink format, using the gid as sample name
	call = "./plink --23file "+ f + " F" + gid + "ID" + gid + "I 1"
	call += " --out 23andme_plink/genotypeid_" + gid
	print "convert gid " + gid
	subprocess.call(call,shell=True)
	
# this is part of the same script, plink is still in cwd but it crashes, saying 
# "Error: Failed to open /home/bastia.fam"

for i in list_bed:
  # check that files have been processed and are working so far. 
	if os.path.isfile(i.replace(".bed",".fam")) and os.path.isfile(i.replace(".bed",".bim")):
		listhandle.write(cwd + "/"+i.replace(".bed","")+"\n")
call_merge = "./plink --bfile " + cwd + "/" + start_bed + " --merge-list " + cwd + "/merge_list.txt --make-bed --out " + cwd + "/23andme_merged/merge-pass1"
print "merging 23andme data, first pass"
subprocess.call(["./plink","--bfile",cwd+"/"+start_bed,"--merge-list",cwd + "/merge_list.txt","--make-bed","--out",cwd+"/23andme_merged/merge-pass1"])

Put the input files in files. Make sure you directories 23andme_merged and 23andme_plugin exist before running.