#import sys
#import os
import subprocess
import genecounter
import numpy
if (__name__ == '__main__'):
x = 0
y = 0
outdir = '/mnt/lustre/data/users/cusanovich/RNAseq_scripts/bedmakerOE/'
header = ['Chr', 'Start', 'End', 'Gene', 'ExonicLength']
for j in range(1, 12):
fcno = str(j)
fcid = 'FlowCell' + fcno + '/'
print fcid
finlist = genecounter.findiv_grabber(fcid)
print finlist[0]
samples = []
for ids in finlist: #['163802','168851']:#
countslist = genecounter.lane_grabber(fcid, ids)
samples.extend(countslist)
# print samples[0:11]
for sample in samples:
#print sample
fcnum = '.fc0' + str(fcno)
if int(fcno) > 9:
fcnum = '.fc' + str(fcno)
samp = sample.split('/')[-2] + '.' + sample.split('/')[-1].split(
'.')[0] + fcnum
if(__name__=='__main__'):
x = 0
y = 0
z = 1
fclist = []
outdir = '/mnt/lustre/data/users/cusanovich/RNAseq_scripts/bedmakerOE/'
header = ['Chr', 'Start', 'End', 'Gene', 'ExonicLength']
for j in range(1,12):
if x == 1:
header = []
z = 0
fcno = str(j)
fcid = 'FlowCell' + fcno + '/'
print fcid
finlist = genecounter.findiv_grabber(fcid)
print finlist[0]
samples = []
for ids in finlist:#['163802','168851']:#
countslist = genecounter.lane_grabber(fcid,ids)
samples.extend(countslist)
# print samples[0:11]
for sample in samples:
#print sample
fcnum = '.fc0' + str(fcno)
if int(fcno) > 9:
fcnum = '.fc' + str(fcno)
samp = sample.split('/')[-2] + '.' + sample.split('/')[-1].split('.')[0] + fcnum
header.append(samp)