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How to use read_rv method in fMBT
Best Python code snippet using fMBT_python
QC_1.smk
Source:QC_1.smk 
1#!/usr/bin/env python2'''3Pre-processing of metaG and metaT data step - quality reads filtering4Authors: Carmen Saenz, Mani Arumugam5'''6#7# configuration yaml file8# import sys9import os.path10from os import path11# args = sys.argv12# config_path = args[args.index("--configfile") + 1]13config_path = 'configuration yaml file' #args[args_idx+1]14print(" *******************************")15print(" Reading configuration yaml file: ")#, config_path)16print(" *******************************")17print(" ")18# Variables from configuration yaml file19if config['PROJECT'] is None:20 print('ERROR in ', config_path, ': PROJECT variable is empty. Please, complete ', config_path)21else:22 project_id = config['PROJECT']23if config['working_dir'] is None:24 print('ERROR in ', config_path, ': working_dir variable is empty. Please, complete ', config_path)25elif path.exists(config['working_dir']) is False:26 print('WARNING in ', config_path, ': working_dir path does not exit. The directory will be created by MIntO')27 working_dir = config['working_dir']28else:29 working_dir = config['working_dir']30if config['omics'] in ('metaG', 'metaT'):31 omics = config['omics']32else:33 print('ERROR in ', config_path, ': omics variable is not correct. "omics" variable should be metaG or metaT.')34if config['local_dir'] is None:35 print('ERROR in ', config_path, ': local_dir variable is empty. Please, complete ', config_path)36else:37 local_dir = config['local_dir']38if config['raw_reads_dir'] is None:39 print('ERROR in ', config_path, ': raw_reads_dir variable in configuration yaml file is empty. Please, complete ', config_path)40else:41 raw_dir = config['raw_reads_dir']42if config['minto_dir'] is None:43 print('ERROR in ', config_path, ': minto_dir variable in configuration yaml file is empty. Please, complete ', config_path)44elif path.exists(config['minto_dir']) is False:45 print('ERROR in ', config_path, ': minto_dir variable path does not exit. Please, complete ', config_path)46else:47 minto_dir=config["minto_dir"]48 script_dir=config["minto_dir"]+"/scripts"49if config['METADATA'] is None:50 print('WARNING in ', config_path, ': METADATA variable is empty. Samples will be analyzed excluding the metadata.')51 metadata=config["METADATA"]52 #metadata="None"53elif config['METADATA'] == "None":54 print('WARNING in ', config_path, ': METADATA variable is empty. Samples will be analyzed excluding the metadata.')55 metadata=config["METADATA"]56if config['METADATA'] is not None:57 if path.exists(config['METADATA']) is False:58 print('ERROR in ', config_path, ': METADATA variable path does not exit. Please, complete ', config_path)59 else:60 metadata=config["METADATA"]61# Make list of illumina samples, if ILLUMINA in config62if 'ILLUMINA' in config:63 if config['ILLUMINA'] is None:64 print('ERROR in ', config_path, ': ILLUMINA list of samples is empty. Please, complete ', config_path)65 else:66 try:67 # Make list of illumina samples, if ILLUMINA in config68 ilmn_samples = list()69 if 'ILLUMINA' in config:70 #print("Samples:")71 for ilmn in config["ILLUMINA"]:72 if path.exists(raw_dir+'/'+ilmn+'/'+ilmn+'.1.fq.gz') is True:73 #print(ilmn)74 ilmn_samples.append(ilmn)75 else:76 raise TypeError('ERROR in ', config_path, ': ILLUMINA list of samples does not exist. Please, complete ', config_path)77 except: 78 print('ERROR in ', config_path, ': ILLUMINA list of samples does not exist or has an incorrect format. Please, complete ', config_path)79else:80 print('ERROR in ', config_path, ': ILLUMINA list of samples is empty. Please, complete ', config_path)81if config['trimmomatic_adaptors'] in ('False', 'Skip'):82 pass83elif config['trimmomatic_adaptors'] is None:84 print('ERROR in ', config_path, ': trimmomatic_adaptors variable is empty. Please, complete ', config_path)85elif path.exists(config['trimmomatic_adaptors']) is False:86 print('ERROR in ', config_path, ': trimmomatic_adaptors variable path does not exit. Please, complete ', config_path)87if config['perc_remaining_reads'] is None:88 print('ERROR in ', config_path, ': perc_remaining_reads variable is empty. Please, complete ', config_path)89if config['TRIMMOMATIC_threads'] is None:90 print('ERROR in ', config_path, ': TRIMMOMATIC_threads variable is empty. Please, complete ', config_path)91elif type(config['TRIMMOMATIC_threads']) != int:92 print('ERROR in ', config_path, ': TRIMMOMATIC_threads variable is not an integer. Please, complete ', config_path)93if config['TRIMMOMATIC_memory'] is None:94 print('ERROR in ', config_path, ': TRIMMOMATIC_memory variable is empty. Please, complete ', config_path)95elif type(config['TRIMMOMATIC_memory']) != int:96 print('ERROR in ', config_path, ': TRIMMOMATIC_memory variable is not an integer. Please, complete ', config_path)97# Define all the outputs needed by target 'all'98def qc1_trim_quality_output():99 result = expand("{wd}/{omics}/1-trimmed/{sample}/{sample}.{group}.paired.fq.gz", 100 wd = working_dir,101 omics = omics,102 sample = config["ILLUMINA"] if "ILLUMINA" in config else [],103 group=['1', '2']),\104 expand("{wd}/{omics}/1-trimmed/{sample}/{sample}.{group}.single.fq.gz", 105 wd = working_dir,106 omics = omics,107 sample = config["ILLUMINA"] if "ILLUMINA" in config else [],108 group=['1', '2']),\109 expand("{wd}/{omics}/1-trimmed/{sample}/{sample}_trimlog_quality_adapter", 110 wd = working_dir,111 omics = omics,112 sample = config["ILLUMINA"] if "ILLUMINA" in config else [])113 return(result)114def qc1_check_read_length_output():115 result = expand("{wd}/{omics}/1-trimmed/{sample}/{sample}.{group}.read_length.txt", 116 wd = working_dir,117 omics = omics,118 sample = config["ILLUMINA"] if "ILLUMINA" in config else [],119 group = ['1', '2']),\120 expand("{wd}/{omics}/1-trimmed/samples_read_length.txt",121 wd = working_dir,122 omics = omics)123 return(result)124def qc1_read_length_cutoff_output():125 result = expand("{wd}/output/1-trimmed/{omics}_cumulative_read_lenght_cutoff.pdf", 126 wd = working_dir,127 omics = omics)128 return(result)129def qc1_config_yml_output():130 result = expand("{wd}/{omics}/QC_2.yaml", 131 wd = working_dir,132 omics = omics)133 return(result)134rule all:135 input:136 qc1_trim_quality_output(),137 qc1_check_read_length_output(),138 qc1_read_length_cutoff_output(),139 qc1_config_yml_output()140###############################################################################################141# Pre-processing of metaG and metaT data 142# Filter reads by quality143############################################################################################### 144rule qc1_trim_quality:145 input:146 read_fw=lambda wildcards: '{raw_dir}/{sample}/{sample}.1.fq.gz'.format(raw_dir=raw_dir, sample = wildcards.sample),147 read_rv=lambda wildcards: '{raw_dir}/{sample}/{sample}.2.fq.gz'.format(raw_dir=raw_dir, sample = wildcards.sample),148 output: 149 pairead1="{wd}/{omics}/1-trimmed/{sample}/{sample}.1.paired.fq.gz", 150 singleread1="{wd}/{omics}/1-trimmed/{sample}/{sample}.1.single.fq.gz", 151 pairead2="{wd}/{omics}/1-trimmed/{sample}/{sample}.2.paired.fq.gz", 152 singleread2="{wd}/{omics}/1-trimmed/{sample}/{sample}.2.single.fq.gz", 153 log_adapter="{wd}/{omics}/1-trimmed/{sample}/{sample}_trimlog_quality_adapter"154 params:155 tmp_quality=lambda wildcards: "{local_dir}/{omics}_{sample}_qc1_trim_quality/".format(local_dir=local_dir, omics = omics, sample = wildcards.sample),156 adapters=config['trimmomatic_adaptors'],157 log: 158 "{wd}/logs/{omics}/1-trimmed/{sample}_qc1_trim_quality.log"159 resources:160 mem=config['TRIMMOMATIC_memory']161 threads:162 config['TRIMMOMATIC_threads'] 163 conda: 164 config["minto_dir"]+"/envs/MIntO_base.yml"#trimmomatic165 shell: 166 """mkdir -p {params.tmp_quality}1-trimmed/167 remote_dir=$(dirname {output.pairead1})168 adapter_file="{params.adapters}"169time (if [ "{params.adapters}" == "Skip" ]170 then echo ${{adapter_file}}; \171cat {input.read_fw} > {output.pairead1}; \172> {output.singleread1}; \173cat {input.read_rv} > {output.pairead2}; \174> {output.singleread2}; \175> {output.log_adapter}176elif [ "{params.adapters}" == "False" ]177 then echo 'Generate adapter sequences file'; \178sh {script_dir}/index_adapter.sh {input.read_fw} {wildcards.sample} {params.tmp_quality}1-trimmed/ {wildcards.wd} {wildcards.omics}; \179trimmomatic PE -threads {threads} -trimlog {params.tmp_quality}1-trimmed/{wildcards.sample}_trimlog_quality_adapter -phred33 {input.read_fw} {input.read_rv} \180{params.tmp_quality}1-trimmed/{wildcards.sample}.1.paired.fq.gz {params.tmp_quality}1-trimmed/{wildcards.sample}.1.single.fq.gz \181{params.tmp_quality}1-trimmed/{wildcards.sample}.2.paired.fq.gz {params.tmp_quality}1-trimmed/{wildcards.sample}.2.single.fq.gz \182TRAILING:5 LEADING:5 SLIDINGWINDOW:4:20 ILLUMINACLIP:{params.tmp_quality}1-trimmed/adapters.fa:2:30:10:2:keepBothReads; \183rsync {params.tmp_quality}1-trimmed/* $remote_dir184else echo 'Filter by quality'185 trimmomatic PE -threads {threads} -trimlog {params.tmp_quality}1-trimmed/{wildcards.sample}_trimlog_quality_adapter -phred33 {input.read_fw} {input.read_rv} \186{params.tmp_quality}1-trimmed/{wildcards.sample}.1.paired.fq.gz {params.tmp_quality}1-trimmed/{wildcards.sample}.1.single.fq.gz \187{params.tmp_quality}1-trimmed/{wildcards.sample}.2.paired.fq.gz {params.tmp_quality}1-trimmed/{wildcards.sample}.2.single.fq.gz \188TRAILING:5 LEADING:5 SLIDINGWINDOW:4:20 ILLUMINACLIP:${{adapter_file}}:2:30:10:2:keepBothReads; \189rsync {params.tmp_quality}1-trimmed/* $remote_dir190 fi ) >& {log}191 rm -rf {params.tmp_quality}"""192 193rule qc1_check_read_length:194 input: 195 pairead="{wd}/{omics}/1-trimmed/{sample}/{sample}.{group}.paired.fq.gz"196 output: 197 length="{wd}/{omics}/1-trimmed/{sample}/{sample}.{group}.read_length.txt"198 params:199 tmp_read_length=lambda wildcards: "{local_dir}/{omics}_{sample}.{group}_qc1_check_read_length/".format(local_dir=local_dir, omics = omics, sample = wildcards.sample, group = wildcards.group),200 log: 201 "{wd}/logs/{omics}/1-trimmed/{sample}.{group}.check_read_length.log"202 resources:203 mem=config['TRIMMOMATIC_memory']204 threads:205 config['TRIMMOMATIC_threads'] 206 shell: 207 """ mkdir -p {params.tmp_read_length}208 time (sh {script_dir}/QC_trim_read_length.sh {input.pairead} {params.tmp_read_length}/{wildcards.sample}.{wildcards.group}.read_length.txt {wildcards.sample}_{wildcards.group}209 rsync {params.tmp_read_length}/{wildcards.sample}.{wildcards.group}.read_length.txt {output.length}) >& {log}210 rm -rf {params.tmp_read_length} """211rule qc1_check_read_length_merge:212 input: 213 length=expand("{{wd}}/{{omics}}/1-trimmed/{sample}/{sample}.{group}.read_length.txt", sample=ilmn_samples, group=['1', '2'])214 output: 215 list_samples="{wd}/{omics}/1-trimmed/samples_read_length.txt", 216 log: 217 "{wd}/logs/{omics}/1-trimmed/qc1_check_read_length_merge.log"218 resources:219 mem=config['TRIMMOMATIC_memory']220 threads:221 config['TRIMMOMATIC_threads'] 222 shell: 223 """time (cat {input.length} >> {output.list_samples}) >& {log}""" 224 225rule qc1_cumulative_read_len_plot:226 input:227 list_samples="{wd}/{omics}/1-trimmed/samples_read_length.txt", 228 output:229 plot="{wd}/output/1-trimmed/{omics}_cumulative_read_lenght_cutoff.pdf", 230 cutoff_file="{wd}/{omics}/1-trimmed/QC_1_min_len_read_cutoff.txt"231 params: 232 cutoff=config["perc_remaining_reads"], 233 log: 234 "{wd}/logs/{omics}/1-trimmed/plot_cumulative_read_len.log"235 resources:236 mem=config['TRIMMOMATIC_memory']237 threads:238 config['TRIMMOMATIC_threads'] 239 conda: 240 config["minto_dir"]+"/envs/taxa_env.yml"241 shell:242 """ time (Rscript {script_dir}/QC_cumulative_read_length_plot.R {input.list_samples} {params.cutoff} {output.plot} {output.cutoff_file}) >& {log}""" #; rm {input.list_length}243 244##########################################################################################################245# Generate configuration yml file for the next step in pre-processing of metaG and metaT data 246##########################################################################################################247rule qc1_config_yml_file:248 input: 249 cutoff_file="{wd}/{omics}/1-trimmed/QC_1_min_len_read_cutoff.txt",250 output: 251 config_file="{wd}/{omics}/QC_2.yaml"252 params: 253 tmp_qc1_yaml=lambda wildcards: "{local_dir}/{omics}_qc1_config_yml_file/".format(local_dir=local_dir, omics = omics),254 trim_threads=config['TRIMMOMATIC_memory'],255 trim_memory=config['TRIMMOMATIC_threads'] 256 resources:257 mem=2258 threads: 259 2260 log: 261 "{wd}/logs/{omics}/qc1_config_yml_file.log"262 shell: 263 """264 mkdir -p {params.tmp_qc1_yaml}265 time (files='{ilmn_samples}'; echo $files; echo $files| tr ' ' '\\n'| sed 's/^/- /' - > {params.tmp_qc1_yaml}/samples_illumina.txt266echo "######################267# General settings268######################269PROJECT: {project_id}270working_dir: {wildcards.wd}271omics: {wildcards.omics}272local_dir: {local_dir}273minto_dir: {minto_dir}274METADATA: {metadata}275######################276# Program settings277######################278# Pre-processing - length reads filtering279TRIMMOMATIC_threads: {params.trim_threads}280TRIMMOMATIC_memory: {params.trim_memory}" > {params.tmp_qc1_yaml}QC_2.yaml281cat {input.cutoff_file} >> {params.tmp_qc1_yaml}QC_2.yaml282echo "283# Pre-processing - host genome filtering284PATH_host_genome:285NAME_host_genome:286BWA_index_host_threads:287BWA_index_host_memory:288BWA_host_threads:289BWA_host_memory: " >> {params.tmp_qc1_yaml}QC_2.yaml290if [ "{omics}" == "metaG" ];\291 then echo "292# Assembly-free taxonomy profiling293TAXA_threads:294TAXA_memory:295taxa_profile: metaphlan">> {params.tmp_qc1_yaml}QC_2.yaml296elif [ "{omics}" == "metaT" ];\297 then echo "298# ribosomal RNA depletion299sortmeRNA_threads:300sortmeRNA_memory:301sortmeRNA_db:302sortmeRNA_db_idx: ">> {params.tmp_qc1_yaml}QC_2.yaml303fi304echo "305# Input data306# ILLUMINA section:307# -----------------308# List of illumina samples that will be filtered by read length.309#310# E.g.:311# - I1312# - I2313#314ILLUMINA:" >> {params.tmp_qc1_yaml}QC_2.yaml315cat {params.tmp_qc1_yaml}/samples_illumina.txt >> {params.tmp_qc1_yaml}QC_2.yaml316rsync {params.tmp_qc1_yaml}QC_2.yaml {output.config_file}) >& {log}317rm -rf {params.tmp_qc1_yaml}318 """ 319 ...
client.py
Source:client.py
...156 Returns return value of the expr.157 Raises RemoteEvalError if expr caused an exception.158 """159 return self.exec_in(namespace, "", expr, async=async, lock=lock)160 def read_rv(self, async_rv, timeout=0):161 """Read return value of async call.162 Parameters:163 async_rv (string or Async_rv object)164 Handle to asynchronous return value, created by165 async exec_in or eval_in.166 timeout (float or integer, optional)167 -1: block until return value is ready and return it.168 0: returns pythonshare.Busy immediately if return169 value is not readable yet.170 > 0: wait until this timeout (NOT IMPLEMENTED).171 The defualt is 0.172 """173 if isinstance(async_rv, str):174 async_rv = eval(async_rv)175 rv = self.eval_in(async_rv.ns, "pythonshare_ns.read_rv(%s)" % (async_rv,))176 return rv177 def export_ns(self, namespace):178 """Export namespace to remote peer179 Parameters:180 namespace (string)181 Namespace to be exported, can be local or182 remote to current host.183 Returns True on success or raises an exception. If succeeded,184 this connection becomes a server for requests from remote185 peer. (The remote peer accesses registered namespace through186 this connection object.)187 """188 pythonshare._send(Register_ns(namespace), self._to_server)189 rv = pythonshare._recv(self._from_server)190 if isinstance(rv, Ns_rv) and rv.status:191 return True192 else:193 raise pythonshare.PythonShareError(rv.errormsg)194 def import_ns(self, namespace):195 """196 """197 pythonshare._send(Request_ns(namespace), self._to_server)198 rv = pythonshare._recv(self._from_server)199 if isinstance(rv, Ns_rv) and rv.status:200 return True201 else:202 raise pythonshare.PythonShareError(rv.errormsg)203 def drop_ns(self, namespace):204 """Delete namespace from the remote peer205 Parameters:206 namespace (string)207 Namespace to be dropped, can be local or208 remote to the server.209 Returns True on success or raises an exception.210 """211 pythonshare._send(Drop_ns(namespace), self._to_server)212 rv = pythonshare._recv(self._from_server)213 if isinstance(rv, Ns_rv) and rv.status:214 return True215 else:216 raise pythonshare.PythonShareError(rv.errormsg)217 def unlock_ns(self, namespace):218 """Unlock namespace on the remote peer219 Parameters:220 namespace (string)221 Namespace to be unlocked, can be local or222 remote to the server.223 Returns True on success or raises an exception.224 """225 pythonshare._send(Server_ctl("unlock", namespace), self._to_server)226 rv = pythonshare._recv(self._from_server)227 if isinstance(rv, Server_ctl_rv) and rv.status == 0:228 return True229 else:230 raise pythonshare.PythonShareError(rv.message)231 def poll_rvs(self, namespace=None):232 """Poll available async return values from namespace.233 Parameters:234 namespace (string, optional)235 namespace from which return values are queried.236 The default is returned by namespace().237 Example:238 rv = c.eval_("time.sleep(1)", async=True)239 print c.poll_rvs(rv.ns)240 time.sleep(1)241 print c.poll_rvs(rv.ns)242 print c.read_rv(rv)243 """244 return self.eval_in(namespace, "pythonshare_ns.poll_rvs()",245 async=False, lock=False)246 def close(self):247 pythonshare._check_hook("before:client.socket.close", {"socket": self._s})248 pythonshare._close(self._to_server, self._from_server, self._s)249 def kill_server(self, namespace=None):250 """Send server shutdown message"""251 if namespace == None:252 namespace = self.namespace()253 pythonshare._send(Server_ctl("die", namespace), self._to_server)254 return True255 def ls_local(self):256 """List local namespaces on the server"""...
RV.py
Source:RV.py
...5import astropy.units as u6import astropy.constants as const7##This sctipt will compute the mass and radius of our planet8#Uses the results of our lightcurve analysis.9def read_rv():10 ##Reads in RV data11 ##returns arrays of times and radial velocities12 fname = "RV_data.txt"13 f = open(fname)14 time = []15 rv = []16 17 18 for i in f.readlines():19 if i[0] == "#":20 continue21 22 time.append(float(i.split()[0]))23 rv.append(float(i.split()[1]))24 25 26 27 return time , rv28 29def Prior(X):30 #I ultimately decided to use a uniform prior here31 return 132 33def lsq(X , D):34 ##A least-squares based fitting function.35 t = D[0]36 rv = D[1]37 38 ls = 039 for i in range(len(t)):40 ls += ( X[2] * np.sin(t[i] * 2 * np.pi / X[0] + X[1]) - rv[i]) ** 241 42 return -1 * ls * Prior(X)43 44def Q(X):45 ##This is our sampling distribution46 47 cov = [ [0.08 , 0 , 0] , [0, 1e-1 ,0 ] , [0 , 0 , 10 ] ]48 mean = [0 , 0 , 0]49 Y = X + np.random.multivariate_normal(mean , cov)50 51 52 while min(Y) < 0:53 Y = X + np.random.multivariate_normal(mean , cov)54 55 return Y56 57def plot_fit(t , rv , X):58 ##This code will plot our raadial velocity data set and our fit to the data59 60 fx = []61 fy = []62 63 for i in np.linspace(t[0] , t[-1] , 10000):64 fx.append(i)65 fy.append(X[2] * np.sin(i * 2 * np.pi / X[0] + X[1]))66 #print (fy)67 plt.plot(fx , fy)68 plt.scatter(t , rv)69 plt.show()70 71def measure():72 ##Measures and returns our R and M estimate73 tr = 2454955.78837374 75 phi = tr * 2 * np.pi / (3.55)76 77 t , rvel = read_rv()78 79 DI = 0.004380 Rstar = 1.7981 82 Rp = np.sqrt(Rstar ** 2 * DI)83 84 print (Rp)85 86 87 88 x0 = [3.55 , 4.34505429e+06 , 2.50998989e+02]89 opt = MCMC.MCMC(lsq , [t , rvel] )90 opt.M_H(Q , 5000 , x0 )91 print (opt.MAP , opt.MAPL)...
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