import sys
import os
from hivwholeseq.utils.generic import mkdirs
from hivwholeseq.patients.samples import itersample
from hivwholeseq.sequencing.samples import load_samples_sequenced as lss
from hivwholeseq.patients.samples import load_samples_sequenced as lssp
from hivwholeseq.sequencing.filenames import get_sample_foldername
# Script
if __name__ == '__main__':
samples_pat = lssp()
samples_seq = lss()
for samplename, sample in itersample(samples_pat):
root_foldername = sample.get_foldername()+'samples_sequencing/'
mkdirs(root_foldername)
for samplenameseq, sampleseq in samples_seq.iterrows():
if sampleseq['patient sample'] == samplename:
src_folder = get_sample_foldername(samplenameseq)
dst_folder = root_foldername+samplenameseq
if not os.path.islink(dst_folder):
os.symlink(src_folder, dst_folder)
print 'Symlink:', src_folder, dst_folder
else:
print 'Esists:', dst_folder
def make_symlinks(dataset, VERBOSE=0):
'''Make symlinks for fastq.gz from the SRA'''
seq_run = dataset.name
samples = dataset.samples
data_folder = get_seqrun_foldername(seq_run)
raw_root_folder = dataset.loc['raw data']
import re
seq_run_int = int(re.findall(r'\d+$', seq_run)[0])
# Unclassified reads
unclass_fn = '/'.join(raw_root_folder.split('/')[:-2])+'/'
for fn in os.listdir(unclass_fn):
if ('illumina_M' in fn) and ('RunId'+'{:04d}'.format(seq_run_int) in fn):
unclass_fn = unclass_fn+fn+'/LaneId1/'
break
fn1 = unclass_fn+[fn for fn in os.listdir(unclass_fn) if 'L001_R1' in fn][0]
fn2 = unclass_fn+[fn for fn in os.listdir(unclass_fn) if 'L001_R2' in fn][0]
dst_folder = data_folder+foldername_adapter(-1)
dst_fn1 = dst_folder+'read1.fastq.gz'
dst_fn2 = dst_folder+'read2.fastq.gz'
if not os.path.isfile(dst_fn1):
os.symlink(fn1, dst_fn1)
elif VERBOSE:
print dst_fn1, 'exists already'
if not os.path.isfile(dst_fn2):
os.symlink(fn2, dst_fn2)
elif VERBOSE:
print dst_fn2, 'exists already'
if VERBOSE:
print 'Unclassified reads symlinked'
# Samples
for sn, sample in samples.iterrows():
if 'missing SRA' in str(sample['notes']):
continue
if str(sample['raw name']) != 'nan':
raw_fn = str(sample['raw name'])
elif str(sample['patient sample']) != 'nan':
raw_fn = str(sample['patient sample'])
else:
raw_fn = str(sample.name)
tmp = [fn for fn in os.listdir(raw_root_folder) if raw_fn in fn]
if not tmp:
print 'FAILED:', raw_fn
print 'LISTDIR:', '\n'.join(os.listdir(raw_root_folder))
raise ValueError('Folder not found')
sample_fn = raw_root_folder+tmp[0]+'/'
fn1 = sample_fn+[fn for fn in os.listdir(sample_fn) if 'L001_R1' in fn][0]
fn2 = sample_fn+[fn for fn in os.listdir(sample_fn) if 'L001_R2' in fn][0]
adaID = sample['adapter']
dst_folder = data_folder+foldername_adapter(adaID)
dst_fn1 = dst_folder+'read1.fastq.gz'
dst_fn2 = dst_folder+'read2.fastq.gz'
if not os.path.isfile(dst_fn1):
os.symlink(fn1, dst_fn1)
elif VERBOSE:
print dst_fn1, 'exists already'
if not os.path.isfile(dst_fn2):
os.symlink(fn2, dst_fn2)
elif VERBOSE:
print dst_fn2, 'exists already'
if VERBOSE:
print sn+' '+adaID+' reads symlinked'
# Symlink samples folder to runs folder
src_folder = data_folder+foldername_adapter(adaID).rstrip('/')
dst_folder = get_sample_foldername(sample.name).rstrip('/')
if not os.path.islink(dst_folder):
os.symlink(src_folder, dst_folder)
elif VERBOSE:
print dst_folder, 'exists already'
