walterst

#!/usr/bin/env python

# Modified from Greg Caporaso's code in qiime/split_libraries_fastq.py

# Usage:  python compare_fastq_labels.py fastq1_fp fastq2_fp

from itertools import izip
from sys import argv

from cogent.parse.fastq import MinimalFastqParser

walterst

#!/usr/bin/env python

""" Usage:
python add_taxa_to_fasta.py input_taxa_file input_fasta_file output_fasta
"""

from sys import argv

from cogent.parse.fasta import MinimalFastaParser

walterst

#!/usr/bin/env python

# USAGE
# python create_majority_taxonomy.py X Y Z A
# where X is the taxonomy mapping file for all NR seqs, Y is the representative
# file (i.e. one of the rep_set/ files with the 119 release), Z is the OTU 
# mapping file created from running pick_otus.py, and A is the output 
# consensus mapping file

from sys import argv

walterst

#!/usr/bin/env python

# USAGE
# python create_consensus_taxonomy.py X Y Z A
# where X is the taxonomy mapping file for all NR seqs, Y is the representative
# file (i.e. one of the rep_set/ files with the 119 release), Z is the OTU 
# mapping file created from running pick_otus.py, and A is the output 
# consensus mapping file

from sys import argv

walterst

#!/usr/bin/env python


# Usage:  python filter_barcode_header.py original_barcode_seqs.fastq new_barcode_seqs.fastq
# WARNING-the second file specified will be overwritten if it exists!

bc_start_indicator = "1:N:0:"
chars_to_strip = ["+"]

from sys import argv

walterst

#!/usr/bin/env python

# Used to filter a fastq to match another fastq that is a subset of the query one, e.g. matching a
# index fastq to the pear assembled subset fastq
# Usage:  python filter_fastq.py input_fastq target_fastq output_fastq

from sys import argv

from cogent.parse.fastq import MinimalFastqParser

walterst

#!/usr/bin/env python

# Used to count fastq seqs in gzipped files, write counts and file name to log file
# Usage:  python count_zipped_fastq_reads.py fastq_folder log_file
# where fastq_folder has all of the fastq files in it (doesn't search subdirectories)

from sys import argv
from glob import glob

from cogent.parse.fastq import MinimalFastqParser

walterst

#!/usr/bin/env python

# Used to filter a fastq to match another fastq that is a subset of the query one, e.g. matching a
# index fastq to the pear assembled subset fastq
# Usage:  python filter_fastq.py input_fastq target_fastq output_fastq

from sys import argv

from cogent.parse.fastq import MinimalFastqParser
from qiime.util import gzip_open

walterst

#!/usr/bin/env python

__author__ = "William Walters"
__copyright__ = "Copyright 2011"
__credits__ = ["William Walters"]
__license__ = "GPL"
__version__ = "1.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
 

walterst

#!/usr/bin/env python

# Usage:
# python split_taxonomy_by_domain.py  A X Y Z
# where A is the original raw SILVA taxonomy (tab separated seq ID<tab>semicolon separated taxonomy 
# X is the input taxonomy mapping file (e.g. consensus/majority, or other parsed taxonomy file)
# Y is the output 16S mapping file, Z is the output 18S mapping file.

from sys import argv