| Previous changeset 1:1e9797878349 (2015-06-29) Next changeset 3:8e1efafa6277 (2015-08-12) |
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Commit message:
Fix pysam version in riboplot (was 0.7.7 instead of 0.8.3). Fix move sys import to the top in ribocount.py, riboplot.py. Minor: * Include an empty conditional when no RNA coverage is required. * Remove output directories after zip file is created. |
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modified:
data/riboplot.html ribocount.xml riboplot.xml riboplot/ribocount.py riboplot/riboplot.py |
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| diff -r 1e9797878349 -r b6fd86c539ea data/riboplot.html --- a/data/riboplot.html Mon Jun 29 17:12:15 2015 +0100 +++ b/data/riboplot.html Thu Jul 02 11:53:59 2015 +0100 |
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| @@ -41,13 +41,13 @@ <p> <img width="100%" class="u-max-full-width" src="ribograph.png"/><br> <p> - <h4>Download plots<br> + <h5>Download plots<br> <a href="ribograph.png">PNG</a>, <a href="ribograph.svg">SVG</a> - </h4> + </h5> - <h4>Download counts<br> + <h5>Download counts<br> <a href="RiboCounts.csv">RiboCounts.csv</a> - </h4> + </h5> <p> <small> (Right click --> Save link/target as...) |
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| diff -r 1e9797878349 -r b6fd86c539ea ribocount.xml --- a/ribocount.xml Mon Jun 29 17:12:15 2015 +0100 +++ b/ribocount.xml Thu Jul 02 11:53:59 2015 +0100 |
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| @@ -7,7 +7,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">./riboplot/ribocount.py + <command interpreter="python">riboplot/ribocount.py --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}" |
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| diff -r 1e9797878349 -r b6fd86c539ea riboplot.xml --- a/riboplot.xml Mon Jun 29 17:12:15 2015 +0100 +++ b/riboplot.xml Thu Jul 02 11:53:59 2015 +0100 |
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| @@ -3,12 +3,12 @@ </description> <requirements> <requirement type="package" version="1.2.1">matplotlib</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> + <requirement type="package" version="0.8.3">pysam</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">./riboplot/riboplot.py + <command interpreter="python">riboplot/riboplot.py --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --transcript_name "${transcript_name}" @@ -41,6 +41,7 @@ <when value="yes"> <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> </when> + <when value="no" /> </conditional> <param name="read_length" type="integer" label="Read length to consider" value="28"/> <param name="read_offset" type="integer" label="Offset" value="0"/> |
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| diff -r 1e9797878349 -r b6fd86c539ea riboplot/ribocount.py --- a/riboplot/ribocount.py Mon Jun 29 17:12:15 2015 +0100 +++ b/riboplot/ribocount.py Thu Jul 02 11:53:59 2015 +0100 |
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| @@ -1,4 +1,6 @@ # check dependencies +import sys + missing_deps = [] try: import pysam @@ -11,8 +13,7 @@ \n\n{}\n'''.format('\n'.join(missing_deps))) import os -import sys -import timeit +# import timeit import shutil import zipfile import logging @@ -141,10 +142,12 @@ for name in f: zip.write(os.path.join(root, name)) + shutil.rmtree(output_path) logging.debug('Writing HTML report') with open(os.path.join(CONFIG.DATA_DIR, 'ribocount_index.html')) as j, open(args.html_file, 'w') as k: k.write(j.read().format(count=count, read_length=read_length)) if __name__ == '__main__': - print timeit.timeit('main()', number=1, setup='from __main__ import main') + # print timeit.timeit('main()', number=1, setup='from __main__ import main') + main() |
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| diff -r 1e9797878349 -r b6fd86c539ea riboplot/riboplot.py --- a/riboplot/riboplot.py Mon Jun 29 17:12:15 2015 +0100 +++ b/riboplot/riboplot.py Thu Jul 02 11:53:59 2015 +0100 |
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| @@ -1,4 +1,6 @@ # check dependencies +import sys + missing_deps = [] try: import pysam @@ -21,10 +23,9 @@ import os import re -import sys import config import pysam -import timeit +# import timeit import shutil import logging import tempfile @@ -316,4 +317,5 @@ if __name__ == '__main__': - print timeit.timeit('main()', number=1, setup='from __main__ import main') + # print timeit.timeit('main()', number=1, setup='from __main__ import main') + main() |