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  • Committer: Bazaar Package Importer
  • Author(s): Steffen Moeller
  • Date: 2010-12-04 22:30:35 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20101204223035-j11kinhcrrdgg2p2
Tags: 1.5-1
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
  - major additions to Cookbook
  - added AlleleFreqs attribute to ensembl Variation objects.
  - added getGeneByStableId method to genome objects.
  - added Introns attribute to Transcript objects and an Intron class.
  - added Mann-Whitney test and a Monte-Carlo version
  - exploratory and confirmatory period estimation techniques (suitable for
    symbolic and continuous data)
  - Information theoretic measures (AIC and BIC) added
  - drawing of trees with collapsed nodes
  - progress display indicator support for terminal and GUI apps
  - added parser for illumina HiSeq2000 and GAiix sequence files as 
    cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
  - added parser to FASTQ files, one of the output options for illumina's
    workflow, also added cookbook demo.
  - added functionality for parsing of SFF files without the Roche tools in
    cogent.parse.binary_sff
  - thousand fold performance improvement to nmds
  - >10-fold performance improvements to some Table operations

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Lines of Context:
tests/data/fastq.txt
 
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@GAPC_0015:6:1:1259:10413#0/1
 
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AACACCAAACTTCTCCACCACGTGAGCTACAAAAG
 
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+GAPC_0015:6:1:1259:10413#0/1
 
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````Y^T]`]c^cabcacc`^Lb^ccYT\T\Y\WF
 
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@GAPC_0015:6:1:1283:11957#0/1
 
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TATGTATATATAACATATACATATATACATACATA
 
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+GAPC_0015:6:1:1283:11957#0/1
 
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]KZ[PY]_[YY^```ac^\\`bT``c`\aT``bbb
 
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@GAPC_0015:6:1:1284:10484#0/1
 
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TCAGTTTTCCTCGCCATATTTCACGTCCTAAAGCG
 
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+GAPC_0015:6:1:1284:10484#0/1
 
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UM_]]U_]Z_Y^\^^``Y]`^SZ]\Ybb`^_LbL_
 
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@GAPC_0015:6:1:1287:17135#0/1
 
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TGTGCCTATGGAAGCAGTTCTAGGATCCCCTAGAA
 
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+GAPC_0015:6:1:1287:17135#0/1
 
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^aacccL\ccc\c\cTKTS]KZ\]]I\[Wa^T`^K
 
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@GAPC_0015:6:1:1293:3171#0/1
 
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AAAGAAAGGAAGAAAAGAAAAAGAAACCCGAGTTA
 
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+GAPC_0015:6:1:1293:3171#0/1
 
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b`bbbU_[YYcadcda_LbaaabWbaacYcc`a^c
 
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@GAPC_0015:6:1:1297:10729#0/1
 
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TAATGCCAAAGAAATATTTCCAAACTACATGCTTA
 
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+GAPC_0015:6:1:1297:10729#0/1
 
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T\ccLbb``bacc]_cacccccLccc\ccTccYL^
 
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@GAPC_0015:6:1:1299:5940#0/1
 
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AATCAAGAAATGAAGATTTATGTATGTGAAGAATA
 
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+GAPC_0015:6:1:1299:5940#0/1
 
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dcddbcfffdfffd`dd`^`c`Oc`Ybb`^eecde
 
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@GAPC_0015:6:1:1308:6996#0/1
 
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TGGGACACATGTCCATGCTGTGGTTTTAACCGGCA
 
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+GAPC_0015:6:1:1308:6996#0/1
 
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a]`aLY`Y^^ccYa`^^TccK_X]\c\c`caTTTc
 
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@GAPC_0015:6:1:1314:13295#0/1
 
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AATATTGCTTTGTCTGAACGATAGTGCTCTTTGAT
 
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+GAPC_0015:6:1:1314:13295#0/1
 
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cLcc\\dddddaaYd`T```bLYT\`a```bZccc
 
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@GAPC_0015:6:1:1317:3403#0/1
 
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TTGTTTCCACTTGGTTGATTTCACCCCTGAGTTTG
 
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+GAPC_0015:6:1:1317:3403#0/1
 
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\\\ZTYTSaLbb``\_UZ_bbcc`cc^[ac\a\T\