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gzip support #35

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gzip support #35

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1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ taxonomy ID. Additional options are specified below.
Optional:
* `-o2, --output2 OUTPUT.FASTA.............`second output FASTA/Q file with extracted seqs (for paired reads)
* `--fastq-output..........................`Instead of producing FASTA files, print FASTQ files (requires FASTQ input)
* `--gzip-output...........................`Gzip output
* `--exclude...............................`Instead of finding reads matching specified taxids, finds reads NOT matching specified taxids.
* `-r, --report MYFILE.KREPORT.............`Kraken report file (required if specifying --include-children or --include-parents)
* `--include-children......................`include reads classified at more specific levels than specified taxonomy ID levels.
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8 changes: 6 additions & 2 deletions combine_kreports.py
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Expand Up @@ -54,6 +54,7 @@
# - main
# - process_kraken_report
####################################################################
import gzip
import os, sys, argparse
import operator
from time import gmtime
Expand Down Expand Up @@ -197,8 +198,11 @@ def main():
sys.stdout.write("\r\t%i/%i samples processed" % (count_samples, num_samples))
sys.stdout.flush()
id2files[count_samples] = r_file
#Open File
curr_file = open(r_file,'r')
#Open File
if r_file.endswith(".gz"):
curr_file = gzip.open(r_file,'rt')
else:
curr_file = open(r_file, 'r')
for line in curr_file:
report_vals = process_kraken_report(line)
if len(report_vals) < 5:
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25 changes: 19 additions & 6 deletions extract_kraken_reads.py
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Expand Up @@ -172,6 +172,8 @@ def main():
parser.add_argument('--fastq-output', dest='fastq_out', required=False,
action='store_true',default=False,
help='Print output FASTQ reads [requires input FASTQ, default: output is FASTA]')
parser.add_argument('--gzip-output', dest='gzip_output', required=False,
action='store_true', default=False)
parser.set_defaults(append=False)

args=parser.parse_args()
Expand Down Expand Up @@ -343,13 +345,24 @@ def main():
sys.stdout.flush()
#Open output file
if (args.append):
o_file = open(args.output_file, 'a')
if args.output_file2 != '':
o_file2 = open(args.output_file2, 'a')
if not args.gzip_output:
o_file = open(args.output_file, 'a')
if args.output_file2 != '':
o_file2 = open(args.output_file2, 'a')
else:
o_file = gzip.open(args.output_file, 'wta')
if args.output_file2 != '':
o_file2 = gzip.open(args.output_file2, 'wta')
else:
o_file = open(args.output_file, 'w')
if args.output_file2 != '':
o_file2 = open(args.output_file2, 'w')
if not args.gzip_output:
o_file = open(args.output_file, 'w')
if args.output_file2 != '':
o_file2 = open(args.output_file2, 'w')
else:
o_file = gzip.open(args.output_file, 'wt')
if args.output_file2 != '':
o_file2 = gzip.open(args.output_file2, 'wt')

#Process SEQUENCE 1 file
count_seqs = 0
count_output = 0
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