Added MultiBLAST.py and .gitignore

Author: Kronopt

.gitignore

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+# Pycharm files
+.idea/

MultiBLAST.py

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+#!/usr/bin/env python
+# coding: utf-8
+
+"""
+MultiBLAST
+Sequentially Blast every fasta file (.faa or .fas) on a folder against a local database
+
+DEPENDENCIES:
+    - Python 2.7
+    - Blast+ executables (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+    - LINUX (tested and developed on Ubuntu 14.0.4, but will most likely work on WINDOWS and MAC too)
+
+HOW TO RUN:
+    - Organize your files as follows on a folder:
+        - MultiBLAST.py
+        - database files (obtained via makeblast, with 'makeblastdb -in [yourGenes].pfasta -dbtype prot')
+        - folder with fasta files (.faa or .fas) to blast (must be the only existing folder in the directory)
+    - Run MultiBLAST.py from the command-line as follows 'python MultiBLAST.py [-t [#]]'
+    - For more help, type 'python MultiBLAST.py -h'
+
+ENSURES:
+    - Each fasta file will be blasted against the given database
+    - Each blast output is created inside the fasta folder
+"""
+
+import os
+import argparse
+from time import time, strftime, localtime
+from sys import exit
+
+__author__ = 'Pedro HC David, https://github.com/Kronopt'
+__credits__ = ['Pedro HC David']
+__version__ = '1.0'
+__date__ = '00:17h, 21/10/2016'
+__status__ = 'Finished'
+
+
+def blast(threads):
+    """
+    Main Function
+
+    PARAMETERS:
+        threads : int/str
+            Number of CPU threads to use
+
+    REQUIRES:
+        threads must be a number >= 1
+
+    ENSURES:
+        Blast each file against the given database
+    """
+
+    root_folder, root_list = root_files()
+
+    # Obtains root path, database name and a list containing all the fasta failes
+    folder_root_dir = fasta_folder(root_list)
+    db = db_file(root_list)
+    fasta_files = fasta_files_folder(root_folder, folder_root_dir)
+
+    start_blast_text()
+    
+    # Timer, START
+    start = time()
+
+    # Time of program start
+    program_start_time = strftime('%d/%m/%y  %H:%M:%S', localtime())
+
+    # Main loop
+    loop_blast(fasta_files, root_folder, folder_root_dir, db, threads)
+    end_blast_text(start, program_start_time)
+
+
+def exit_script():
+    """
+    Exits the script
+    """
+    
+    print
+    print '*****'
+    print 'EXITING SCRIPT'
+    print '*****'
+    exit()
+
+
+# -----------------------------------------------------
+# FILES AND FOLDERS SECTION
+# -----------------------------------------------------
+
+
+def root_files():
+    """
+    Creates a list of every file/folder in the current working directory (ROOT)
+    """
+    
+    root_folder = os.getcwd()
+    root_list = os.listdir(root_folder)
+    root_list.sort()
+
+    return root_folder, root_list
+
+
+def fasta_folder(root_list):
+    """
+    Name of the folder containing the fasta files (.faa or .fas) files
+    Prints the folder to the screen
+
+    PARAMETERS:
+        root_list : list of str
+            List of directories in the root directory
+
+    REQUIRES:
+        Directories must be valid
+
+    ENSURES:
+        Path to the only folder in the root directory
+    """
+
+    print
+    
+    folder_root_dir = filter(lambda x: os.path.isdir(x), root_list)
+    if len(folder_root_dir) != 1:
+        print 'ERROR: None or more than one folder was found'
+        exit_script()
+
+    print 'FASTA FOLDER:'
+    print '    ', folder_root_dir[0]
+    print
+
+    return folder_root_dir[0]
+
+
+def db_file(root_list):
+    """
+    Database files
+    Prints the name of the database to the screen
+
+    PARAMETERS:
+        root_list : list of str
+            List of directories in the root directory
+
+    REQUIRES:
+        Directories must be valid
+
+    ENSURES:
+        Path to the .pfasta database file
+    """
+    
+    db = filter(lambda x: x.endswith('.pfasta'), root_list)
+    if len(db) != 1:
+        print 'ERROR: None or more than one database file was found'
+        exit_script()
+
+    print 'DB FILE:'
+    print '    ', db[0]
+    print
+
+    return db[0]
+
+
+def fasta_files_folder(root_folder, folder_root_dir):
+    """
+    Fasta files
+    Prints every file name to the screen
+
+    PARAMETERS:
+        root_folder : str
+            Root folder's path
+        folder_root_dir : str
+            Fasta file folder's name
+
+    REQUIRES:
+        root_folder must be a valid directory
+        folder_root_dir must be a valid folder name
+
+    ENSURES:
+        List of fasta files
+    """
+
+    fasta_files = filter(lambda x: (x.endswith('.faa') or x.endswith('.fas'))
+                         and os.path.isfile(root_folder + '/' + folder_root_dir + '/' + x),
+                         os.listdir(root_folder + '/' + folder_root_dir))
+    fasta_files.sort()
+
+    print 'FASTA FILES:'
+    for faa_file in fasta_files:
+        print '    ', faa_file
+    print
+
+    return fasta_files
+
+
+# -----------------------------------------------------
+# blast SECTION
+# -----------------------------------------------------
+
+
+def start_blast_text():
+    """
+    Start blast text
+    """
+    
+    print
+    print '*****'
+    print 'STARTING BLASTS'
+    print '*****'
+    print
+    print
+
+
+def loop_blast(fasta_files, root_folder, folder_root_dir, db, threads):
+    """
+    Main code for blasting each fasta file
+    Prints information on each successful blast
+
+    PARAMETERS:
+        fasta_files : list of str
+            List of fasta files
+        root_folder : str
+            Path to root folder
+        folder_root_dir : str
+            Fasta folder's name
+        db : str
+            Database name
+        threads : str/int
+            Number of CPU threads to use
+
+    REQUIRES:
+        fasta_files must have a list of existing fasta files
+        root_folder must be a valide directory
+        folder_root_dir must be the name of an existing folder
+        db must be the name of the existing database
+        threads must be a number >= 1
+
+    ENSURES:
+        Blast of each fasta file agains the local specified database
+    """
+
+    count = 1
+    for fasta_file in fasta_files:
+
+        # Timer, START
+        start = time()
+        
+        print '------------------'
+        print 'blast', count, 'out of', len(fasta_files)
+        print 'BLASTING:'
+        print '    ', fasta_file
+
+        out_file_name = fasta_file[:len(fasta_file) - 4] + '__' + db[0:-7] + '_OUT'
+
+        # Tries to blast
+        standard_blast = 'blastp -out ' + out_file_name + ' -outfmt 6 -query "' + root_folder + '/' + \
+                         folder_root_dir + '/' + fasta_file + '" -db ' + db + ' -num_threads ' + str(threads)
+        
+        try:
+            os.system(standard_blast)
+        except:
+            print
+            print 'ERROR: Could not run NCBI blast+ program blastp'
+            exit_script()
+
+        # Timer, END
+        end = time()
+
+        days, hours, minutes, seconds = sec_to_hours(end - start)
+
+        print
+        print 'TIME ELAPSED:'
+        if days != 0:
+            print str(days) + 'd ',
+        print str(hours) + 'h', str(minutes) + 'm', str(seconds) + 's'
+        print
+
+        # Moves the output file to the output file folder
+        os.rename(out_file_name, folder_root_dir + '/' + out_file_name)
+
+        count += 1
+
+
+def end_blast_text(timer_start, program_start):
+    """
+    End blast text
+
+    PARAMETERS:
+        timer_start : float
+            Value obtained from time.time()
+        program_start : str
+            Current time in text format
+
+    ENSURES:
+        Time information printed to the screen
+    """
+
+    days, hours, minutes, seconds = sec_to_hours(time() - timer_start)
+    program_end = strftime('%d/%m/%y  %H:%M:%S', localtime())
+    
+    print '------------------'
+    print 'TIME OF START/END:'
+    print program_start
+    print program_end
+    print
+    print 'DURATION:'
+    if days != 0:
+        print str(days) + 'd ',
+    print str(hours) + 'h', str(minutes) + 'm', str(seconds) + 's'
+    print
+    print
+    print '*****'
+    print 'END OF BLASTS'
+    print '*****'
+    print
+
+
+def sec_to_hours(seconds):
+    """
+    Converts seconds into hours (or days, if it takes that long to run)
+
+    PARAMETERS:
+        seconds : int/str/float
+            number of seconds
+
+    REQUIRES:
+        seconds must be a number >= 1
+
+    ENSURES:
+        Seconds translated into days, hours, minutes and seconds
+    """
+
+    seconds = int(seconds)
+    
+    days = seconds / 86400
+    hours = (seconds - days * 86400) / 3600
+    minutes = (seconds - days * 86400 - hours * 3600) / 60
+    seconds = (seconds - days * 86400 - hours * 3600 - minutes * 60)
+
+    return days, hours, minutes, seconds
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Blasts fasta files (.faa or .fas) to a local database. '
+                                                 'Organize your files so that the root folder has only: [1] this '
+                                                 'script (MultiBLAST.py); [2] all the database files (obtained via '
+                                                 '"makeblastdb -in [yourGenes].pfasta -dbtype prot"); [3] folder with '
+                                                 'fasta files (.faa or .fas) to blast (must be the only folder '
+                                                 'available)')
+    parser.add_argument('-t', metavar='#', nargs='?', default=1, type=int, const=1, help='Number of CPU threads')
+    arguments = parser.parse_args()
+
+    blast(arguments.t)