comparison pre_sartools.py @ 4:05c9b1a7f44e draft default tip

Uploaded new release 1.7.3

3:de6d0b7c17af

        counts_files.write("label\tfiles\tgroup\n")
        for (level, filename, label) in inputs:
            filename_base = basename(filename)
            # For RSEM files we process files as HTSeq count output
            tmpdir = tempfile.mkdtemp()
            with open(filename, 'rb') as csvfile:
                with open(join(tmpdir, basename(filename)), 'wb') as out:
                    spamwriter = csv.writer(out, delimiter='\t')
                    reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
                    if len(reader.fieldnames) > 2:
                        for row in reader:
                            spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))

4:05c9b1a7f44e

        counts_files.write("label\tfiles\tgroup\n")
        for (level, filename, label) in inputs:
            filename_base = basename(filename)
            # For RSEM files we process files as HTSeq count output
            tmpdir = tempfile.mkdtemp()
            with open(filename, 'rt') as csvfile:
                with open(join(tmpdir, basename(filename)), 'wt') as out:
                    spamwriter = csv.writer(out, delimiter='\t')
                    reader = csv.DictReader(csvfile, delimiter='\t', skipinitialspace=True)
                    if len(reader.fieldnames) > 2:
                        for row in reader:
                            spamwriter.writerow((row['gene_id'], int(float(row['expected_count']))))