104 lines
3.1 KiB
Python
104 lines
3.1 KiB
Python
#!/usr/bin/env python
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# This code is to concatenate the batch GO Term Finder results (.tsv) generated from batch GTF perl code(Chris Johnson, U of Tulsa) into a list table
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import os
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import glob
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def list_files(directory):
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"""Return a list of all files in the given directory."""
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return glob.glob(os.path.join(directory, '*.txt.tsv'))
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def concatenate_gtf_results(data_dir, output_file):
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"""Concatenate the GTF results into a single file."""
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output = open(output_file, 'w')
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files = list_files(data_dir)
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files.sort()
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for file_path in files:
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file_name = os.path.basename(file_path).rstrip('.txt.tsv')
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with open(file_path, 'r') as f:
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labels = f.readline().strip().split('\t')
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output.write('\t'.join(labels) + '\n')
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for line in f:
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line = line.strip().strip('\t')
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if line:
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output.write(line + '\n')
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output.close()
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if __name__ == '__main__':
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if len(sys.argv) != 3:
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print('Usage: python Concatenate_GTF_results.py data_dir output_file')
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sys.exit(1)
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data_dir = sys.argv[1]
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output_file = sys.argv[2]
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concatenate_gtf_results(data_dir, output_file)
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# Old version
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# def list_files(directory):
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# """Return a list of all files in the given directory."""
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# return glob.glob(os.path.join(directory, '*.txt.tsv'))
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# try:
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# data_file_Path = sys.argv[1]
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# output_file_Path = sys.argv[2]
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# except:
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# print ('Usage: python Concatenate_GTF_results.py /datasetPath /outputFilePath_and_Name')
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# print ('Data file not found, error in given directory')
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# sys.exit(1)
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# try:
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# output = open(output_file_Path, 'w')
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# except OSError:
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# print ('output file error')
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# # get all the GTF result files in given directory
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# File_list = []
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# File_list = list_files(data_file_Path)
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# File_list.sort()
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# i = 0
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# for file in File_list:
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# #parse the file names given in absolute path
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# file_name = file.strip().split('/')[-1]
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# file_name = file_name.rstrip('.txt.tsv')
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# # function to read tsv files from a given directory
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# #open the file
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# data = open(file,'r')
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# #reading the label line
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# labelLine = data.readline()
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# label = labelLine.strip().split('\t')
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# #write the label
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# #updates2010July26: update following label writing code
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# if i == 0:
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# # output.write('cluster origin')
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# for element in label:
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# output.write(element)
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# output.write('\t')
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# i = i + 1
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# #updates2010July26 End
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# #switch to the next line
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# output.write('\n')
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# #read the GO terms
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# GOTermLines = data.readlines()
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# for GOTerm in GOTermLines:
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# GOTerm = GOTerm.strip().strip('\t')
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# if GOTerm != '':
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# #updates2010July26: remove the code to write the first column 'REMc cluster ID'
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# #output.write(file_name)
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# #output.write('\t')
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# ##updates2010July26 update end
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# output.write(GOTerm + '\n')
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# #output.write('\n')
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# output.close()
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