Mercurial > repos > peterjc > seq_select_by_id
changeset 25:704454850cfa draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id commit 8ac4eac1507e91426b883d440c89d3f654c51a26-dirty
| author | peterjc |
|---|---|
| date | Wed, 17 May 2017 12:43:21 -0400 |
| parents | a22c48f357df |
| children | f0f2d1894a04 |
| files | tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.py tools/seq_select_by_id/seq_select_by_id.xml |
| diffstat | 3 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/tools/seq_select_by_id/README.rst Wed May 17 09:18:14 2017 -0400 +++ b/tools/seq_select_by_id/README.rst Wed May 17 12:43:21 2017 -0400 @@ -90,6 +90,7 @@ - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. - Python 3 compatible print function. v0.0.13 - Python 3 compatible exception handling. +v0.0.14 - Script works on Python 2 and 3 (fixed output file mode). ======= ======================================================================
--- a/tools/seq_select_by_id/seq_select_by_id.py Wed May 17 09:18:14 2017 -0400 +++ b/tools/seq_select_by_id/seq_select_by_id.py Wed May 17 12:43:21 2017 -0400 @@ -26,7 +26,7 @@ import sys if "-v" in sys.argv or "--version" in sys.argv: - print("v0.0.13") + print("v0.0.14") sys.exit(0) # Parse Command Line @@ -128,7 +128,7 @@ else: # Avoid overhead of parsing into SeqRecord objects, # just re-use the original formatting from the input file. - out_handle = open(out_file, "w") + out_handle = open(out_file, "wb") count = 0 for name in parse_ids(tabular_file, column): try:
--- a/tools/seq_select_by_id/seq_select_by_id.xml Wed May 17 09:18:14 2017 -0400 +++ b/tools/seq_select_by_id/seq_select_by_id.xml Wed May 17 12:43:21 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.13"> +<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.14"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.67">biopython</requirement>