python script modification of LSC0.2.4 ?

[arthur.yxt]

It's really really great news that LSC now takes BWA into usage in the current version of 0.2.4. It took me one whole day only to find out that the master script "runLSC.py" might need some changes in order to run smoothly.

There seem to be some late-night editings on the last part quoted below:
########
old_output_foldername = output_foldername.strip("/") + "_old/"

mv_cmd = "mv " + output_foldername + " " + old_output_foldername
os.system(mv_cmd)

getLR_cmd = bin_path + "getLR.py " + cfg_filename
os.system(getLR_cmd)

os.system("cp " + old_output_foldername + "corrected_LR_SR.map.fa " + output_foldername
os.system("cp " + old_output_foldername + "uncorrected_LR_SR.map.fa " + output_foldername
os.system("cp " + old_output_foldername + "full_LR_SR.map.fa " + output_foldername + "oldfull_LR_SR.map.fa"

correct_fullfa_cmd = bin_path + "correct_fullfa.py " + output_foldername + "corrected_LR_SR.map.fa " + output_foldername + "uncorrected_LR_SR.map.fa " + output_foldername + "oldfull_LR_SR.map.fa " + output_foldername + "newLR.fa " + output_foldername + "full_LR_SR.map.fa_ > " + output_foldername + "correct_fullfa.log"
os.system(correct_fullfa_cmd)

cat_cmd = "cat " + output_foldername + "full_LR_SR.map.fa_ " + output_foldername + "full_LR_SR.map.fa_2 > " + output_foldername + "full_LR_SR.map.fa"
os.system(cat_cmd)
########


This might work?
########
old_output_foldername = output_foldername.strip("/") + "_old/"

mv_cmd = "mv " + output_foldername + " " + old_output_foldername
os.system(mv_cmd)


getLR_cmd = "python " + bin_path + "getLR.py " + cfg_filename
# getLR.py will mkdir named "output_foldername"
os.system(getLR_cmd)

os.system("cp " + old_output_foldername + "corrected_LR_SR.map.fa " + output_foldername)
os.system("cp " + old_output_foldername + "uncorrected_LR_SR.map.fa " + output_foldername)
os.system("cp " + old_output_foldername + "full_LR_SR.map.fa " + output_foldername + "oldfull_LR_SR.map.fa")


correct_fullfa_cmd = "python " + bin_path + "correct_fullfa.py " + output_foldername + "corrected_LR_SR.map.fa " + output_foldername + "uncorrected_LR_SR.map.fa " + output_foldername + "oldfull_LR_SR.map.fa " + output_foldername + "newLR.fa " + output_foldername + "full_LR_SR.map.fa_ > " + output_foldername + "correct_fullfa.log"
os.system(correct_fullfa_cmd)

cat_cmd = "cat " + output_foldername + "full_LR_SR.map.fa_ " + output_foldername + "full_LR_SR.map.fa_2 > " + output_foldername + "full_LR_SR.map.fa"
os.system(cat_cmd)
########


I know the adding of the "python" here seems to be redundant, but I got this error otherwise:
###
sh: /data/chen/arthur/Joerg/pacbio/LSC/bin/getLR.py: not found
###

Again, great work! Cheers!