multiple_join_paired_ends.py – Run join_paired_ends.py on multiple files.

Description:

This script runs join_paired_ends.py on data that are already demultiplexed (split up according to sample, with one sample per pair of files). The script supports the following types of input:

• a directory containing many files, where each file is named on a per-sample basis
• a directory containing many directories, where each directory is named on a per-sample basis

The script assumes that the leading/trailing characters before/after the read number indicator (see –read1_indicator) are matched between forward and reverse reads. For example:

• S0_L001_R1_001.fastq.gz and S0_L001_R2_001.fastq.gz would be matched up reads
• S0_L002_R1_00X.fastq.gz and S0_L002_R2_00X.fastq.gz would be matched up reads

If an optional –barcode_indicator file is used, it is searched for in the same manner that the paired files are searched for, so if the default “_I1_” is used, S0_L001_R1_001.fastq.gz and S0_L001_R2_001.fastq.gz would be matched up with S0_L001_I1_001.fastq.gz as the barcode indicator file.

The output directory used for each call to join_paired_ends.py uses the base name of the input read 1 fastq file (a single directory would be problematic since the output names for join_paired_ends.py can be the same for different calls). Use the parameter –include_input_dir_path to also include the input directory name in the output directory path, which may be preferable in the case of an input folder of folders, and –remove_filepath_in_name can be used in this case to prevent the input read 1 fastq file base name from being used as part of the output directory name.

Usage: multiple_join_paired_ends.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_dir

Input directory of directories, or directory of paired fastq files.

-o, --output_dir

Base output directory to write output folders

[OPTIONAL]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior of join_paired_ends.py. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters [default: join_paired_ends.py defaults will be used]

--read1_indicator

Substring to search for to indicate read 1 [default: _R1_]

--read2_indicator

Substring to search for to indicate read 2 [default: _R2_]

-b, --match_barcodes

Enable searching for matching barcodes [default: False]

--barcode_indicator

Substring to search for to indicate barcode reads [default: _I1_]

--leading_text

Leading text to add to each join_paired_ends.py command [default: no leading text added]

--trailing_text

Trailing text to add to each join_paired_ends.py command [default: no trailing text added]

--include_input_dir_path

Include the input directory name in the output directory path. Useful in cases where the file names are repeated in input folders [default: False]

--remove_filepath_in_name

Disable inclusion of the input filename in the output directory names. Must use –include_input_dir_path if this option is enabled [default: False]

-w, --print_only

Print the commands but don’t call them – useful for debugging [default: False]

Output:

The output of running join_paired_ends.py on many input files. See script description for more details.

Example 1:

Process an input folder of paired-up files (by filename, with the default _R1_ and _R2_ containing the forward and reverse reads filenames, respectively). An optional parameters file is passed with -p. This file can specify an optional parameter for join_paired_ends.py, such as: join_paired_ends:pe_join_method SeqPrep

multiple_join_paired_ends.py -i input_files -o output_folder -p qiime_parameters.txt

Example 2:

Process an input folder of folders (with the filenames having _forward_ and _reverse_ containing the forward and reverse read filenames, respectively). The individual folder names are included in the output folder names, but not the filenames. A matching barcode fastq file (indicated by _barcode_) is also included.

multiple_join_paired_ends.py -i input_folders -o output_folder --read1_indicator '_forward_' --read2_indicator '_reverse_' --include_input_dir_path --remove_filepath_in_name -b --barcode_indicator '_barcode_'

Example 3:

To see what commands would be executed by the script without actually running them, use the following command:

multiple_join_paired_ends.py -i input_files -o output_folder -w