예제 #1
0
파일: frag_array.py 프로젝트: bsmithers/hpf
def gather():
    util.debug("Gathering result")
    job_results = results
    paths.ensure(job_results)
    
    
    #aazj00103_05.075_v1_3.bz2  zj001.fasta    zj001.psipred_ss2
    #aazj00109_05.075_v1_3.bz2  zj001.psipred
    aa_pattern = "aa"+name+"(03|09)\_05\.075\_v1\_3$"
    patterns = [aa_pattern]
    for suf in [".fasta", ".psipred", ".psipred_ss2"]:
        patterns.append(name+suf)
    
    try:
        for pattern in patterns:
            print "Pattern ",pattern
            match = paths.find(pattern, scr_job)
            if not match:
                raise "Missing file"
            for path in match:
                if pattern == aa_pattern:
                    print "Filtering Columns %s" % path
                    for line in fileinput.input(path, inplace=1):
                        print " "+line[:47].strip()
                    fileinput.close()
                print "Path ", path
                file = paths.getFile(path)
                dest = paths.join(job_results, file)
                util.copy(path, job_results)
                if pattern == aa_pattern:
                    util.system("bzip2 %s"  % dest)
    except:
        paths.removerf(job_results)
        raise
예제 #2
0
def gather():
    util.debug("Gathering result")
    job_results = results
    paths.ensure(job_results)

    #aazj00103_05.075_v1_3.bz2  zj001.fasta    zj001.psipred_ss2
    #aazj00109_05.075_v1_3.bz2  zj001.psipred
    aa_pattern = "aa" + name + "(03|09)\_05\.075\_v1\_3$"
    patterns = [aa_pattern]
    for suf in [".fasta", ".psipred", ".psipred_ss2"]:
        patterns.append(name + suf)

    try:
        for pattern in patterns:
            print "Pattern ", pattern
            match = paths.find(pattern, scr_job)
            if not match:
                raise "Missing file"
            for path in match:
                if pattern == aa_pattern:
                    print "Filtering Columns %s" % path
                    for line in fileinput.input(path, inplace=1):
                        print " " + line[:47].strip()
                    fileinput.close()
                print "Path ", path
                file = paths.getFile(path)
                dest = paths.join(job_results, file)
                util.copy(path, job_results)
                if pattern == aa_pattern:
                    util.system("bzip2 %s" % dest)
    except:
        paths.removerf(job_results)
        raise
예제 #3
0
def gather():
    global code, task_id

    utilities.debug("Gathering result")
    paths.ensure(results_dir)
    
    # Contents of results directory (3' library, 9' library, fasta, psipred, and psipred_ss2 files). EG:
    #aazj00103_05.075_v1_3.bz2  zj001.fasta    zj001.psipred_ss2
    #aazj00109_05.075_v1_3.bz2  zj001.psipred
    
    # Set "patterns" for results files.
    aa_pattern = "aa"+code+task_id+"(03|09)\_05\.075\_v1\_3$"
    patterns = [aa_pattern]
    for suf in [".fasta", ".psipred", ".psipred_ss2"]:
        patterns.append(code+task_id+suf)
    
    try:
        for pattern in patterns:
            print "Pattern ",pattern
            
            # Find the results file in scr_job_dir
            match = paths.find(pattern, scr_job_dir)
            
            # If a results file matching pattern is not found in the scr_jobs_dir, raise exception.
            if not match:
                raise "Missing file"
            
            # Copy all results files in scr_job_dir to results_dir. 
            for path in match:
                # If the results file is a frag library, format the frag library file.
                if pattern == aa_pattern:
                    print "Filtering Columns of file %s" % path
                    # fileinput.input opens a file for iteration. Defining inplace=1 allows to given file to be
                    # altered "in place": file is backed up, and stdout is then directed to the file. 
                    # Filters the file: writes " " + first 47 chars of the line. (Specific formatting).
                    for line in fileinput.input(path, inplace=1):
                        print " "+line[:47].strip()
                    fileinput.close()
                print "Path ", path
                
                # Copy the result file to results_dir.
                utilities.copy(path, results_dir)
                
                # If the results file is a frag library, bzip it in the results_dir.
                if pattern == aa_pattern:
                    dest = paths.join(results_dir, paths.getFile(path))
                    utilities.system("bzip2 %s"  % dest)
                    
    # If gathering the results files fails, delete the results_dir and exit.
    except:
        paths.removerf(results_dir)
        raise
예제 #4
0
def gather():
    global code, task_id

    utilities.debug("Gathering result")
    paths.ensure(results_dir)

    # Contents of results directory (3' library, 9' library, fasta, psipred, and psipred_ss2 files). EG:
    #aazj00103_05.075_v1_3.bz2  zj001.fasta    zj001.psipred_ss2
    #aazj00109_05.075_v1_3.bz2  zj001.psipred

    # Set "patterns" for results files.
    aa_pattern = "aa" + code + task_id + "(03|09)\_05\.075\_v1\_3$"
    patterns = [aa_pattern]
    for suf in [".fasta", ".psipred", ".psipred_ss2"]:
        patterns.append(code + task_id + suf)

    try:
        for pattern in patterns:
            print "Pattern ", pattern

            # Find the results file in scr_job_dir
            match = paths.find(pattern, scr_job_dir)

            # If a results file matching pattern is not found in the scr_jobs_dir, raise exception.
            if not match:
                raise "Missing file"

            # Copy all results files in scr_job_dir to results_dir.
            for path in match:
                # If the results file is a frag library, format the frag library file.
                if pattern == aa_pattern:
                    print "Filtering Columns of file %s" % path
                    # fileinput.input opens a file for iteration. Defining inplace=1 allows to given file to be
                    # altered "in place": file is backed up, and stdout is then directed to the file.
                    # Filters the file: writes " " + first 47 chars of the line. (Specific formatting).
                    for line in fileinput.input(path, inplace=1):
                        print " " + line[:47].strip()
                    fileinput.close()
                print "Path ", path

                # Copy the result file to results_dir.
                utilities.copy(path, results_dir)

                # If the results file is a frag library, bzip it in the results_dir.
                if pattern == aa_pattern:
                    dest = paths.join(results_dir, paths.getFile(path))
                    utilities.system("bzip2 %s" % dest)

    # If gathering the results files fails, delete the results_dir and exit.
    except:
        paths.removerf(results_dir)
        raise
예제 #5
0
def cleanup():
    paths.removerf(scr_job_dir)
예제 #6
0
파일: fragmentor.py 프로젝트: bsmithers/hpf
 def cleanup(self):
     # Remove working directory and all its contents.
     paths.removerf(self.working_dir)
예제 #7
0
def cleanup():
    paths.removerf(scr_job)