def aln_df(self, infile, align_score):
print("\tRead align file ", infile)
file_sep = '\t' if myIO.file_os(infile).name_suffix() == 'txt' else ','
aln_df = myIO.file_os(infile, file_sep).flat_file_to_df([0,1,11], True)
#print aln_df
#convert to binary matrix
binary_b = pd.DataFrame(np.where(aln_df >= align_score, 1, 0))
#print np.sum(binary_b)
binary_b.index = [str(x).split('_')[1] for x in list(aln_df.index)]
binary_b.columns = [re.sub(',', ';', str(x)) for x in list(aln_df)]
binary_b.fillna(0, inplace=True)
#print binary_b.ix['Rnl2_SPIKEIN']
#print list(binary_b.index)[:10]
'''
##remove subset species, of which alignment score <1
#calculate shared probes
taxon_sums = binary_b.apply(sum, axis=0)
taxons = list(binary_b)
shared_prob=pd.DataFrame(index=taxons, columns=taxons)
for taxon, col in binary_b.iteritems():
shared_prob[taxon]=binary_b.apply(lambda x, y=col: np.dot(y,x), axis=0)/taxon_sums
shared_prob[taxon][taxon]=0
#
tags_df=pd.DataFrame(index=taxons, columns=taxons)
for taxon, col in shared_prob.iteritems():
row=shared_prob.loc[taxon]
tags_df[taxon]=[1 if a!=1 and b==1 else 0 for a, b in zip(col,row)]
sum_tags=tags_df.apply(max, axis=0)
reserved_taxons=list(sum_tags[sum_tags==0].index)
binary_b=binary_b[reserved_taxons]
'''
return binary_b
def match_ensembl_fa(self, gtf_file):
#get order of chr
ref_arr = self.fa_displayid()
#print ref_arr
#export matched gtf
file_head = myIO.file_os(self.biofile).file_prefix()
out_gtf = file_head + '.' + myIO.file_os(gtf_file).name_suffix()
out_obj = open(out_gtf, 'wt') #out_gtf_file
print('Match the first column of {} with {}, => {}'.format(
gtf_file, self.biofile, out_gtf))
for chr_id in ref_arr:
n = 0
#read gtf
in_obj = self.readonly_handle(self.gtf_file)
for line in in_obj:
if not line.startswith('#'):
items = line.split("\t")
seqid = items[0]
if chr_id == seqid:
out_obj.write(line)
n += 1
in_obj.close()
print('{}:{}'.format(chr_id, n))
out_obj.close()
def match_ncbi_fa(self, gtf_file):
#read matched information from gtf_file
seqid_chr = genome(gtf_file).read_ncbi_gff('seqid', 'chromosome')
#out_gtf_file
file_head = myIO.file_os(self.biofile).file_prefix()
out_gtf = file_head + '.' + myIO.file_os(gtf_file).name_suffix()
out_obj = open(out_gtf, 'wt')
#get order of chr
ref_arr = self.fa_displayid()
#export matched gtf
print('Match the first column of {} with {}, => {}'.format(
gtf_file, self.biofile, out_gtf))
for chr_id in ref_arr:
chromosome = re.sub('chr', '', chr_id, flags=re.IGNORECASE)
n = 0
#read gtf
in_obj = self.readonly_handle(self.biofile)
for line in in_obj:
if not line.startswith('#'):
items = line.split("\t")
seqid = items[0]
if seqid in seqid_chr and seqid_chr[seqid] == chromosome:
items[0] = chr_id
myline = "\t".join(items)
out_obj.write(myline)
n += 1
in_obj.close()
print('{}:{}'.format(chr_id, n))
out_obj.close()
def collapse_matrix(self, pars):
infile, outfile, collapse_func=pars
print('t:', outfile)
#read counts_file: pep_df
file_sep = '\t' if myIO.file_os(infile).name_suffix() == 'txt' else ','
pep_df = pd.read_csv(infile, header=0, index_col=0, sep=file_sep, low_memory=False)
#pep_df.index=pep_df.index.astype(str)
sample_names = list(pep_df)
#print(sample_names)
#both column and row names should be string type
pep_df.columns = pep_df.columns.astype(str)
pep_df.index = pep_df.index.astype(str)
#combined pep_df with protein annotation
pep_pro = self.par['annot_df'][['pep_id', 'pro_id']]
#pep_pro['pep_id']=pep_pro['pep_id'].astype(str)
combined_df = pd.merge(pep_df, pep_pro, how='inner', left_index=True, right_on='pep_id')
#group by protein id
group_dict = combined_df.groupby(['pro_id'], as_index=False).groups
collapse = dict()
for protein_id, row_names in group_dict.items():
subdf = pep_df.ix[row_names]
collapse[protein_id] = subdf.apply(collapse_func, axis=0)
#if protein_id =='A0A126':
#print subdf[['CTLA4.BEADS_ONLY.BEADS_ONLY.BEADS_ONLY.20A20G.1', 'CTLA4.BEADS_ONLY.BEADS_ONLY.BEADS_ONLY.20A20G.2']]
#convert to data frame and transpose
cdf = pd.DataFrame(collapse).transpose()
#remove the first column
cdf = np.round(cdf[sample_names], 1)
#reorder by row names
cdf=cdf.loc[self.par['pro_ids']]
#print cdf
#export
file_sep = '\t' if myIO.file_os(outfile).name_suffix() == 'txt' else ','
cdf.to_csv(outfile, index_label='pro_id', sep=file_sep)
return cdf
def phipseq_alignment(self, sample_name):
print('\n######Anslysis of {} will be trigerred!#####'.format(
sample_name))
#initiate sample par
sample_var = dict(self.par)
sample_var['start_time'] = time.time()
#sample name
sample_var['sample_name'] = sample_name
#sample directory
sample_dir = self.par['sample_dirs'][sample_name]
sample_var['sample_dir'] = myIO.dir_os(sample_dir).create_dir()
print('\tSample directory: ', sample_var['sample_dir'])
#raw data
sample_var['sample_raw_files'] = ','.join(
sample_var['sample_to_raw'][sample_name])
print('\tRaw files: ', sample_var['sample_raw_files'])
#export
sample_var['file_head'] = sample_var['sample_dir'] + sample_name
#default same file
sample_var['sample_sam_file'] = sample_var['file_head'] + '.sam'
#file of read counts
sample_var['sample_RC_file'] = sample_var['file_head'] + '_RC.txt'
sample_var['sample_pro_sumRC_file'] = sample_var[
'file_head'] + '_pro_sumRC.txt'
sample_var['sample_pro_maxRC_file'] = sample_var[
'file_head'] + '_pro_maxRC.txt'
#file for saturation analysis
sample_var['sample_saturation_file'] = sample_var[
'file_head'] + '_saturation.txt'
#sample log
sample_var['sample_log'] = sample_var['file_head'] + '.log'
#sequence alignment
if sample_var['phip_alignment'] == 'yes':
print("\n###sequence alignment", sample_var['tool_aligner'])
#output is sam file
if sample_var['tool_aligner'] == 'bowtie1':
myAlign.alignment(sample_var).bowtie1_alignment()
#counts reads
if sample_var['phip_counting'] == 'yes':
#RC matrix by peptides
myAlign.alignment(sample_var).count_reads()
#RC matrix by proteins
if 'file_annotation' in self.par.keys():
self.combine_peptides(sample_var)
#update sample log
sample_times = mySystem.system().get_time(sample_var['start_time'])
sample_times['sample_name'] = sample_name
myIO.file_os(sample_var['sample_log'], '=').line_replace(sample_times)
def download_annot(self,genome_type):
#print genome_type
url = self.url[genome_type]
#get html and the list of files
url_dir, url_files = web(url).ls_html()
#print url_files
#download and decompress genome files
local_chr_files = {}
for file_url in url_files.keys():
gz_file = myIO.file_os(file_url).download(self.out_dir)
#decompress file
ungz_file = myIO.file_os(gz_file).decompress_gz()
local_chr_files[file_url]=ungz_file
return local_chr_files
def file_to_samples(self):
#get all fastq files
raw_files = self.seek_fq(self.par['dir_raw_data'])
print('Number of raw files:', len(raw_files))
#read sample info file
print('Read sample file: ', self.par['file_sample_info'])
in_obj = open(self.par['file_sample_info'], 'rt')
#set connections between raw data and sample_name
for line in in_obj:
line = line.rstrip("\n")
items = line.split(',')
raw_file_name = items[0]
sample_name = items[1]
#print prefix
for raw_file in raw_files:
file_name = myIO.file_os(raw_file).file_name()
#print file_name
if file_name.find(raw_file_name) == 0:
#dict: raw_sample
self.raw_sample[raw_file] = sample_name
#dict: sample_raw
if sample_name in self.sample_raw:
self.sample_raw[sample_name].append(raw_file)
else:
self.sample_raw[sample_name] = [raw_file]
in_obj.close()
def protein_peptides(self):
pro_pep = {}
#read annotation file
annot_dict = myIO.file_os(self.par['file_annotation'], "\t").to_dict2()
if 'Rnl2_SPIKEIN' in annot_dict:
annot_dict['Rnl2_SPIKEIN']['pep_rank'] = 0
in_pro = [annot_dict[p]['pro_id'] for p in annot_dict.keys()]
in_pro = list(set(in_pro))
print('In proteins:{}, In peptides:{}'.format(in_pro.__len__(), annot_dict.keys().__len__()))
##
pro_rank_pep = {}
for pep_id in self.par['pep_ids']:
pro_id = annot_dict[pep_id]['pro_id']
pep_rank = annot_dict[pep_id]['pep_rank']
pep_rank = int(pep_rank) if isinstance(pep_rank, int) else 0
if pro_id in pro_rank_pep:
pro_rank_pep[pro_id][pep_id] = pep_rank
else:
pro_rank_pep[pro_id] = {pep_id:pep_rank}
#print pro_rank_pep[pro_id]
#
pep_num = 0
for pro_id, pep_dict in pro_rank_pep.items():
#print sorted(pep_dict.keys())
peps = sorted(pro_rank_pep[pro_id], key = pro_rank_pep[pro_id].get)
pep_num += len(peps)
pro_pep[pro_id] = ','.join(peps)
#export
print("Number of protein:{}\tNumber of peptides:{}.".format(len(pro_pep.keys()), pep_num))
myDict.basic(pro_pep, self.par['pro_ids']).dict_to_file(self.par['file_pro_pep'], "\t")
#
return pro_pep
def download_annot(self,genome_type):
#print genome_type
url = self.url[genome_type]
#get html
lines = web(url).get_html()
#get the list of files
chr_files = self.single_file(lines)
print(chr_files)
#download and decompress genome files
local_chr_files = {}
for key in chr_files.keys():
gz_file = myIO.file_os(url+chr_files[key]).download(self.out_dir)
#decompress file
ungz_file = myIO.file_os(gz_file).decompress_gz()
local_chr_files[key] = ungz_file
return local_chr_files
def shrink_fq(self, par):
#read relationship between barcode vs sample from sample_file
barcode_sample = myIO.file_os(par['barcode_file'], '\t').to_dict()
#print barcode_sample
#file handle
m = 0
n = 0
F1 = self.readonly_handle(self.biofile)
out1 = open(self.biofile + '.shrink', 'wt')
F2 = self.readonly_handle(par['index_file'])
out2 = open(par['index_file'] + '.shrink', 'wt')
with F1, F2:
#read 4 lines at a time per file
for L1, La, L2, Lb, L3, Lc, L4, Ld in itertools.zip_longest(
*[F1, F2] * 4):
barcode = Lb.rstrip()
#assign record based on barcode
if barcode in barcode_sample.keys():
#output file handle
out1.writelines([L1, L2, L3, L4])
out2.writelines([La, Lb, Lc, Ld])
m += 1
n += 1
F1.close()
F2.close()
out1.close()
out2.close()
print("{}->{}({})".format(n, m, m / n))
def QC_statistics(self):
print("###Quality control: statistics summary")
#print(self.par['sample_names'])
#print(self.par['dir_result'])
stat_dict = collections.defaultdict(dict)
for sample_name in self.par['sample_names']:
sample_log = '{}{}/{}.log'.format(self.par['dir_result'], sample_name, sample_name)
stat_dict[sample_name] = myIO.file_os(sample_log, '=').to_dict()
#convert to data frame
stat_df = pd.DataFrame(stat_dict)
stat_df = stat_df.transpose()
#1: scatter plot 1
sub_df = stat_df[['raw_reads_num', 'unique_aligned_reads_num']].astype(float)/1e6
#print sub_df
plot_par={'df':sub_df, 'title':'raw_reads_vs_aligned_reads',
'picfile':self.par['dir_QC'] + 'raw_reads_vs_aligned_reads.png',
'pch':'o', 'text':'million reads'}
myPlot.plot(plot_par).dotP()
#2: scatter plot 2
stat_df['unique_aligned_percentage'] = sub_df['unique_aligned_reads_num']*100/sub_df['raw_reads_num']
plot_par['df'] = stat_df[['raw_reads_num','unique_aligned_percentage']].astype(float)
plot_par['title'] = 'percentage_aligned_reads'
plot_par['picfile'] = self.par['dir_QC'] + 'percentage_aligned_reads.png'
myPlot.plot(plot_par).dotP()
#3: export to csv file
print('\tSave statistical summary into {}.'.format(self.par['file_stat']))
stat_df.to_csv(self.par['file_stat'], index_label='sample_names')
def sig_polyclonal(self, count_file):
#count_file = args_tuple
print("Polyclonal analysis of ", count_file)
comb_df, pep_df = myCommon.basic(self.par).combine_df(count_file)
#functions
def hits_func(x, peps, threshold, pro_id):
#signficant hits
hits = x[x >= threshold]
#non_overlapping peptides
peps = [str(x) for x in peps]
hit_peps = [str(x) for x in hits.index]
none_overlapped_hits_num = myList.basic(peps).un_neighbours(
hit_peps, return_type='hits_num')
#if none_overlapped_hits_num>1: print "%d,%d" %(len(list(hits.index)), none_overlapped_hits_num)
#if len(hit_peps)>0: print pro_id, peps, hit_peps
#if pro_id == 'Q9YLJ1': print pro_id, peps, hit_peps
return len(list(
hits.index)), none_overlapped_hits_num, ','.join(hit_peps)
#collapse by protein
hits1 = {}
hits2 = {}
#n = 1
for pro_id, row_index in comb_df.groupby('pro_id').groups.items():
#row is protein id
##get protein-peptides annotations
peps_str = self.par['dict_pro_pep'][pro_id]
peps = peps_str.split(',')
#df by protein
sub_df = pep_df.ix[row_index]
#print("{}\t{}".format(pro_id, list(sub_df.index)) )
#hits num beyond zscore threshold
hits_num = sub_df.apply(hits_func,
axis=0,
args=(peps, self.par['zscore_threshold'],
pro_id))
#if pro_id == 'Q9YLJ1': print hits_num
#all number of significant hits
num1 = [h[0] for h in hits_num]
hits1[pro_id] = dict(zip(list(sub_df), list(num1)))
#number of sig hits without overlapping
num2 = [h[1] for h in hits_num]
hits2[pro_id] = dict(zip(list(sub_df), list(num2)))
#if (np.sum(num1))>10:
#pd.set_option('display.max_columns', None)
#pd.set_option('display.max_rows', None)
#print np.matrix(np.round(sub_df))
#print num1
#print num2
#n+ = 1
#if n == 10: break
#export
file_head = myIO.file_os(count_file).file_prefix() + '_polyclonal'
myDict.basic(hits1, self.par['pro_ids']).dict2_to_file(
file_head + '.txt', "\t")
myDict.basic(hits2, self.par['pro_ids']).dict2_to_file(
file_head + '_nonoverlapped.txt', "\t")
def annot_df(self, infile):
file_sep = '\t' if myIO.file_os(infile).name_suffix() == 'txt' else ','
annot_df = pd.read_csv(infile, header=0, index_col=None, sep=file_sep, low_memory=False)
#bother column and row names should be string type
annot_df.index = annot_df['pep_id']
annot_df.index = annot_df.index.astype(str)
#annot_df.columns=self.par['annot_df'].columns.astype(str)
return annot_df
def __init__(self, biofile=None, sep=None):
self.biofile = biofile
#seperate character
if sep is None:
self.sep = ',' if myIO.file_os(
self.biofile).name_suffix() == 'csv' else "\t"
else:
self.sep = sep
self.record_num = 0
def extract_annot(self, left_column, right_column, FUN):
annot_dict = {}
#read annotation file
annot_df = myIO.file_os(self.par['file_annotation'], sep="\t").to_df(header=True, rowname=False)
for index, row in annot_df.iterrows():
key = row[left_column]
value = FUN(row[right_column])
annot_dict[key] = value
#print "%s:%s" % (key, value)
return annot_dict
def QC_hits(self, infile, threshold=None):
print('###Relationship between significant hits and raw read num of ', infile)
file_prefix = '{}{}_'.format(self.par['dir_QC'], myIO.file_os(infile).name_prefix())
if threshold is None: threshold = float(self.par['zscore_threshold'])
#read statistics file
stat_df = pd.read_table(self.par['file_stat'], sep=",", index_col=0, low_memory=False)
stat_df.index = stat_df['sample_name'] #assign row names
stat_df = stat_df.ix[self.par['sample_names']]#order rows by sample_names
raw_reads = stat_df['raw_reads_num']/1e6
#print stat_df[['sample_name','raw_reads_num']]
#read values file
in_df = pd.read_table(infile, sep="\t", index_col=0, low_memory=False)#rownames and colnames
order_df = in_df[self.par['sample_names']].copy()#order columns
#print(order_df.shape)
#plot of raw reads vs number of hits
#print list(order_df)
def func1(x,y=threshold):
sig = x[x>=y]
return len(sig)
hits_num = order_df.apply(func1, axis=0)
#get compared df
comp_df = pd.DataFrame({'A': raw_reads, 'B': hits_num})
comp_df.to_csv(file_prefix+'raw_vs_sighits.csv', sep=',')
#plot
plot_par={'df':comp_df, 'legend':None,
'title': 'Effects of sequencing depth on significant hits',
'picfile': file_prefix + 'raw_vs_sighits.png',
'xlabel':'Number of raw reads (million)',
'ylabel':'Number of signficant hits'}
myPlot.plot(plot_par).dotP()
#plot of raw reads vs mean values of hits
#print list(order_df)
def func2(x,y=threshold):
x = pd.Series(x)
#print list(x)
sig = x[x>=y]
#print list(sig)
sig_mean = np.mean(sig)
return sig_mean
hits_mean = order_df.apply(func2, axis=0)
#print hits_mean
#get compared df
comp_df = pd.DataFrame({'A': raw_reads, 'B': hits_mean})
outfile=file_prefix+'raw_vs_mean_significant_hits.csv'
print('\texport QC to {}.'.format(outfile))
comp_df.to_csv(outfile, sep=',')
#plot
plot_par={'df':comp_df, 'legend':None,
'title': 'Effects of sequencing depth on significant hits',
'picfile': file_prefix + 'raw_vs_mean_significant_hits.png',
'xlabel':'Number of raw reads (million)',
'ylabel':'Mean values of signficant hits'}
myPlot.plot(plot_par).dotP()
def normalize_by_factor(self, annot_file, col_index, col_factor='pro_len'):
#read RC file
#RC_df=pd.read_table(self.biofile, sep=self.sep, index_col=True)
RC_df = myIO.file_os(self.biofile, sep=self.sep).to_df(header=True,
rowname=True)
#print(RC_df.shape)
#read annotation file
#annot_df=pd.read_table(annot_file, sep="\t", index_col=True)
annot_df = myIO.file_os(annot_file, sep="\t").to_df(header=True,
rowname=True)
#print list(annot_df)
sub_annot = annot_df[[col_index,
col_factor]].drop_duplicates([col_index],
take_last=True)
sub_annot.index = list(sub_annot[col_index])
sub_annot = sub_annot.ix[:, 1:] #remove the column with col_index
#print sub_annot
#sort annot_df by row names of RC_df
sub_annot = sub_annot.ix[list(RC_df.index)]
#for missing proteins, pro_len equal ave-pro_len
ave_pro_len = np.mean(sub_annot[col_factor])
pro_len_df = sub_annot.fillna(ave_pro_len)
#print(pro_len_df.shape)
#normalization by aa length of proteins
RC_df.insert(0, col_factor, list(pro_len_df[col_factor]))
normRC_df = RC_df.apply(lambda x: x[1:] / x[0], axis=1)
#scaling normalization by million reads
def norm_func(x):
sum_x = np.sum(x)
norm_x = x * 10e6 / sum_x if sum_x > 0 else x
norm_x = np.round(norm_x)
norm_x = norm_x.astype(int)
return norm_x
normRC_df = normRC_df.apply(norm_func, axis=0)
#print normRC_df
return normRC_df
def standard_df(self, infile, fill=True):
#read txt file
sep = ',' if myIO.file_os(infile).name_suffix() == 'csv' else '\t'
stand_df = pd.read_table(infile,header=0, index_col=0,sep=sep,low_memory=False)
#string of row names
stand_df.index = [str(x) for x in list(stand_df.index)]
stand_df.columns = [str(x) for x in list(stand_df)]
#replace NAN
if fill == True:
stand_df.fillna(0, inplace=True)
return stand_df
def NC_whole_std(self):
print('\tPolynomial regression of std~median across ALL BEADS-ONLY.')
file_prefix = '{}{}_'.format(self.par['dir_result'], myIO.file_os(self.par['file_NC']).name_prefix())
norm_ncfile = file_prefix+'scalingRC.txt'
if os.path.isfile(norm_ncfile):
phip_nc = pd.read_csv(norm_ncfile, sep='\t', index_col=0, low_memory=False)
else:
phip_nc = normalization(self.par, self.par['file_NC'], norm_ncfile).RC_scaling()
#print(phip_nc.shape)
#summary of nc: mean and std
NC=pd.DataFrame({'mean':phip_nc.mean(axis=1), 'median':phip_nc.median(axis=1), \
'std':phip_nc.std(axis=1), 'sum':phip_nc.sum(axis=1)})
NC['median'][NC['median']==0] = np.nan
NC['std'][NC['std']==0] = np.nan
NC['logmedian'] = np.log10(NC['median'])
NC['logstd'] = np.log10(NC['std'])
#NC=NC.replace([np.inf, -np.inf], -10) #an extreme small value
#
#initiate reg_df for regression
#fill out outliers
reg_df = NC.loc[(NC['median']>0),:].copy()
#order for polynomial regression
reg_df = reg_df.sort_values(['logmedian'], ascending=True)
#polynomial regression
formula = 'logstd~logmedian+I(logmedian**2)+I(logmedian**3)'
pn_model = smf.ols(formula, data=reg_df)
pn_fit = pn_model.fit()
#print(pn_fit.params)
reg_df['pred_logstd'] = pn_fit.predict()
reg_df['pred_std'] = 10**pn_fit.predict()
NC['pred_logstd'] = pn_fit.predict({'logmedian':NC['logmedian']})
NC['pred_std'] = 10**NC['pred_logstd']
#refresh total log
#params=dict(pn_fit.params)
#NC_dict = dict([('polynomial_NC_std:' + x, params[x]) for x in params.keys()])
#myIO.file_os(self.par['file_total_log'], '=').line_replace(NC_dict)
#export fitting of std
NC.to_csv(file_prefix+'polynomial_std.csv', header=True, index_label='row_names')
#draw graph
xm=round(np.nanmax(list(NC['logmedian'])))
ym=round(np.nanmax(list(NC['logstd'])))
plot_par={'df': NC[['logmedian','logstd']], 'xlim':(-.5,xm), 'ylim':(-.5,ym),\
'picfile':file_prefix+'polynomial_std.png', 'text':pn_fit.params }
try:
myPlot.plot(plot_par).regressionP(reg_df['logmedian'], reg_df['pred_logstd'])
except ValueError:
print('Failed to drawing pic and save into {}'.format(plot_par['picfile']))
#return fitting model object
return NC, pn_fit
def init_aligner_par(self):
if self.par['tool_aligner'] == 'bowtie1':
self.par['bowtie_aligner'] = self.par['dir_aligner'] + 'bowtie'
self.par['bowtie_builder'] = self.par['dir_aligner'] + 'bowtie-build'
elif self.par['tool_aligner'] == 'bowtie2':
self.par['bowtie_aligner'] = self.par['dir_aligner'] + 'bowtie2'
self.par['bowtie_builder'] = self.par['dir_aligner'] + 'bowtie2-build'
#print self.par['bowtie_aligner'], self.par['bowtie_builder']
#bowtie index
self.par['bowtie_index_name'] = myIO.file_os(self.par['file_ref_fa']).file_prefix()
self.par['bowtie_index'] = self.par['dir_aligner'] + self.par['bowtie_index_name']
def export_df(self, outfile, threshold=10, index_label='row_names'):
print('\texport data frame to ', outfile)
outsep = ',' if outfile.endswith('.csv') else '\t'
self.df.to_csv(outfile, sep=outsep, index_label=index_label)
#draw a scatterplot
counts = self.df.apply(lambda x, y=threshold: len(x[x>=y]), axis=0)
#print counts
plot_par={'list':counts, 'ylabel':'Sample_names', 'xlabel':'Number of hits',
'picfile': myIO.file_os(outfile).file_prefix()+'.png',
'title': 'Number of hits, threshold='+str(threshold) }
myPlot.plot(plot_par).simple_barh()
def raw_to_samples(self):
#get all fastq files
raw_files = self.seek_fq(self.par['dir_raw_data'])
#print raw_files
#connect raw file to sample name
for raw_file in raw_files:
sample_name = myIO.file_os(raw_file).name_prefix()
self.raw_sample[raw_file] = sample_name
if sample_name in self.sample_raw:
self.sample_raw[sample_name].append(raw_file)
else:
self.sample_raw[sample_name] = [raw_file]
def sample_info(self):
sample_pairs = {}
for raw_file, sample_name in self.raw_sample.items():
raw_file_name = myIO.file_os(raw_file).file_name()
group = 'NC' if 'BEADS' in raw_file_name.upper() else 'PhIP'
if not 'unassigned' in raw_file_name:
sample_name = re.sub('_R1', "", sample_name)
pair = '{},{}'.format(raw_file_name, sample_name)
sample_pairs[pair]=group
#export dict to file
print('Generate sample file: ', self.par['file_sample_info'])
#order per record: fastq file name, sample_name, phip_group
myDict.basic(sample_pairs).dict_to_file(self.par['file_sample_info'], ',')
def combine_df(self, counts_file, annot_index='pep_id'):
#read count file
file_sep = '\t' if myIO.file_os(
counts_file).name_suffix() == 'txt' else ','
counts_df = pd.read_table(counts_file,
sep=file_sep,
index_col=0,
low_memory=False)
counts_df.index = [str(x) for x in counts_df.index]
#print 'counts:', counts_df.shape
#print list(counts_df.index)[:20]
#read annotation file
file_sep = '\t' if myIO.file_os(
self.par['file_annotation']).name_suffix() == 'txt' else ','
annot_df = pd.read_table(self.par['file_annotation'],
sep=file_sep,
index_col=None,
low_memory=False)
annot_df.index = [str(x) for x in annot_df[annot_index]]
#print 'annot:', annot_df.shape
#print list(annot_df[annot_index])[:20]
#combine by rows
comb_df = pd.merge(annot_df,
counts_df,
left_index=True,
right_index=True,
how='inner')
comb_df.index = list(comb_df[annot_index])
#comb_df=comb_df.rename(columns={self.par['protein_assoc']:'pro_id'})
#print comb_df[['pep_id','row_name']]
#print comb_df.shape
#sample df
sample_df = comb_df[self.par['sample_names']]
sample_df.index = list(comb_df[annot_index])
return (comb_df, sample_df)
def download_idmapping(self):
#get web file list
url_idmapping = self.url+'knowledgebase/idmapping/by_organism/'
web_dir, web_files = web(url_idmapping).ls_html()
#print web_files
#select file
file_names = filter(lambda x: '.dat.' in x, web_files.values())
file_names.sort()
file_name = mySystem.system().select_key(file_names, 'Select web file')
#download idmapping dat file
url_file = url_idmapping + file_name
local_file = self.out_dir + file_name
web(url_file).download_file(local_file)
#decompress file
ungz_file = myIO.file_os(local_file).decompress_gz()
print('Save ', url_file, ' as ', ungz_file)
return ungz_file
def download_dna(self):
url = self.url['dna_fa']
#get genome files
#get html
lines = web(url).get_html()
chr_files = self.dna_files(lines)
#download and decompress genome files
local_chr_files = {}
for key in chr_files.keys():
self.ver = re.sub(r"\.chromosome.*", '', chr_files[key])
gz_file = myIO.file_os(url+chr_files[key]).download(self.out_dir)
#decompress file
#ungz_file=myIO.file_os(gz_file).decompress_gz()
local_chr_files[key] = gz_file
#combine fa files
out_file = self.out_dir+self.ver+'.fa'
#print out_file
myGenome.genome(out_file).combine_fa(local_chr_files)
return local_chr_files, out_file
def download_dna(self):
#get html
lines = web(self.url['dna_fa']).get_html()
chr_files = self.dna_files(lines)
#download and decompress genome files
local_chr_files = {}
for key in chr_files.keys():
#release version
self.ver = re.sub(r"_chr.*", '', chr_files[key])
url = self.url['dna_fa']+chr_files[key]
gz_file = myIO.file_os(url).download(self.out_dir)
#decompress file
#ungz_file=myIO.file_os(gz_file).decompress_gz()
local_chr_files[key] = gz_file
#combine fa files
out_file = ''.join([self.out_dir, self.ver,'_dna.fa'])
#print out_file
myGenome.genome(out_file).combine_fa(local_chr_files)
return local_chr_files, out_file
def combine_countfiles(self, args_tuple):
#row_names should be None or list type
infile_tail, RC_level, out_file, row_names = args_tuple
#
counting_dict2 = {}
for sample_name in self.par['sample_names']:
#get read counts of a given sample
counting_file = '{}{}/{}{}'.format(self.par['dir_result'], sample_name, sample_name, infile_tail)
sample_dict2 = myIO.file_os(counting_file, '\t').to_dict2()
for ref in sample_dict2.keys():
#print ref
counts = sample_dict2[ref][RC_level]
if ref in counting_dict2:
counting_dict2[ref].update({sample_name:counts})
#print '=='+ref+'=='
else:
counting_dict2[ref] = {sample_name:counts}
#print sample_name, ref,counting_dict2[ref]
#export counting_dict
myDict.basic(counting_dict2).dict2_to_file(out_file=out_file, row_names=row_names)
def trim_fq(self, outdir, seq_start=0, seq_end=0):
file_name = myIO.file_os(self.biofile).file_name()
outfile = outdir + re.sub('\.gz$', '', file_name)
print("Trim fastq files {}, and save new file {}\n".format(
self.biofile, outfile))
#get file handles of the two fastq files, and the output file
F1 = self.readonly_handle(self.biofile)
out_obj = open(outfile, 'wt')
with F1:
#read 4 lines at a time per file
for L1, L2, L3, L4 in zip(*[F1] * 4):
if seq_start > 0:
L2 = L2[seq_start:]
L4 = L4[seq_start:]
#trim the longer reads from 3-end
if seq_end != 0:
L2 = L2.rstrip()
L4 = L4.rstrip()
L2 = L2[:seq_end] + "\n"
L4 = L4[:seq_end] + "\n"
#export to the output file
out_obj.writelines([L1, L2, L3, L4])
'/home/yuan/results_phip',
'/home-4/[email protected]/work/yuan/results_phip'
]
#get all variables.txt
files_var = []
for d in dirs:
if os.path.isdir(d):
files_formula = os.path.join(d,
'*' + file_type + '*/variables.txt')
#print files_formula
files_var += glob.glob(files_formula)
#sub=myIO.dir_os(d).recrusive_files('variables.txt')
#for s in sub:
# if file_type in s: files_var.append(s)
#get all command lines
for index, file_var in enumerate(files_var):
print(index + 1, file_var)
#revise the parameters of variables.txt
myIO.file_os(file_var, '=').line_replace(par)
#parallel processing
#threads number
#pool=mpd.Pool(processes=8)
#pass one argument at a time
#pool.map(phip_thread, files_var)
#pool.close()
#pool.join()
print('\n\n\n\nGreat! The batch running is done!\n\n\n')
#end
