comparison tools/seq_filter_by_id/seq_filter_by_id.py @ 12:85ef5f5a0562 draft default tip

v0.2.9 - Fixed file open mode for Python 3.11 onwards.

11:83a19df00eab

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This script is copyright 2010-2017 by Peter Cock, The James Hutton Institute
(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
See accompanying text file for licence details (MIT license).

Use -v or --version to get the version, -h or --help for help.
"""

)

options, args = parser.parse_args()

if options.version:
    print("v0.2.7")
    sys.exit(0)

in_file = options.input
seq_format = options.format
out_positive_file = options.output_positive

    for x in options.id_list.split():
        ids.add(clean_name(x.strip()))
    print("Have %i unique identifiers from list" % len(ids))
for tabular_file, columns in identifiers:
    file_ids = set()
    handle = open(tabular_file, "rU")
    if len(columns) > 1:
        # General case of many columns
        for line in handle:
            if line.startswith("#"):
                # Ignore comments

12:85ef5f5a0562

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This script is copyright 2010-2023 by Peter Cock, The James Hutton Institute
(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
See accompanying text file for licence details (MIT license).

Use -v or --version to get the version, -h or --help for help.
"""

)

options, args = parser.parse_args()

if options.version:
    print("v0.2.9")
    sys.exit(0)

in_file = options.input
seq_format = options.format
out_positive_file = options.output_positive

    for x in options.id_list.split():
        ids.add(clean_name(x.strip()))
    print("Have %i unique identifiers from list" % len(ids))
for tabular_file, columns in identifiers:
    file_ids = set()
    handle = open(tabular_file)
    if len(columns) > 1:
        # General case of many columns
        for line in handle:
            if line.startswith("#"):
                # Ignore comments