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jlec 13/12/29 00:56:58 |
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Added: biopython-1.62-SffIO.patch |
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Log: |
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sci-biology/biopython: Add additional patch from Martin Mokrejš |
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(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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Revision Changes Path |
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1.1 sci-biology/biopython/files/biopython-1.62-SffIO.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/biopython-1.62-SffIO.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/biopython-1.62-SffIO.patch?rev=1.1&content-type=text/plain |
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Index: biopython-1.62-SffIO.patch |
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=================================================================== |
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--- Bio/SeqIO/SffIO.py.ori 2013-09-25 13:28:51.000000000 +0200 |
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+++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200 |
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@@ -383,7 +383,14 @@ |
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if padding: |
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padding = 8 - padding |
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if handle.read(padding).count(_null) != padding: |
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- raise ValueError("Post quality %i byte padding region contained data" |
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+ import warnings |
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+ from Bio import BiopythonParserWarning |
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+ warnings.warn("Your SFF file is valid but post quality %i byte " |
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+ "padding region contains UNUSED data. Was the " |
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+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " |
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+ "It did not clear some internal buffer while writing " |
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+ "out new data so that previous values remained in the" |
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+ "output unless overwritten by new real values." |
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% padding) |
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#print read, name, record_offset |
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yield name, record_offset |
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--- Bio/SeqIO/SffIO.py.ori 2013-09-25 14:07:14.000000000 +0200 |
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+++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200 |
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@@ -596,7 +596,14 @@ |
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if padding: |
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padding = 8 - padding |
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if handle.read(padding).count(_null) != padding: |
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- raise ValueError("Post quality %i byte padding region contained data" |
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+ import warnings |
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+ from Bio import BiopythonParserWarning |
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+ warnings.warn("Your SFF file is valid but post quality %i byte " |
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+ "padding region contains UNUSED data. Was the " |
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+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " |
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+ "It did not clear some internal buffer while writing " |
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+ "out new data so that previous values remained in the" |
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+ "output unless overwritten by new real values." |
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% padding) |
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#Follow Roche and apply most aggressive of qual and adapter clipping. |
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#Note Roche seems to ignore adapter clip fields when writing SFF, |
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