Recent changes to filtering.py

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Tue, 24 Jul 2012 14:43:52 -0000

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Tue, 24 Jul 2012 10:29:39 -0000

--- v7
+++ v8
@@ -2,7 +2,9 @@
 
 Quality filtering: 
 
-The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
+This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
+
+Test files associated with this script:
 
 [testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 14:13:41 -0000

--- v6
+++ v7
@@ -4,8 +4,8 @@
 
 The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
 
-[testfile1_filtering.fa]() testing for DNA alphabet with records consisting of protein alphabet and "N"s
+[testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s
 
-[testfile2_filtering.txt]() is a text file in a non-fasta format
+[testfile2_filtering.txt] is a text file in a non-fasta format
 
-[testfile3_filtering.fa]() containing one record of >100bp and another <100bp
+[testfile3_filtering.fa] containing one record of >100bp and another <100bp

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:55:35 -0000

--- v5
+++ v6
@@ -1,11 +1,11 @@
-(filtering.py)[https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py]
+[filtering.py](https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py)
 
 Quality filtering: 
 
 The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
 
-[testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s
+[testfile1_filtering.fa]() testing for DNA alphabet with records consisting of protein alphabet and "N"s
 
-[testfile2_filtering.txt] is a text file in a non-fasta format
+[testfile2_filtering.txt]() is a text file in a non-fasta format
 
-[testfile3_filtering.fa] containing one record of >100bp and another <100bp
+[testfile3_filtering.fa]() containing one record of >100bp and another <100bp

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:54:06 -0000

--- v4
+++ v5
@@ -1,6 +1,7 @@
 (filtering.py)[https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py]
 
 Quality filtering: 
+
 The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
 
 [testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:53:24 -0000

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:52:51 -0000

--- v2
+++ v3
@@ -1,4 +1,4 @@
-(filtering.py) [https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py]
+(filtering.py)[https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py]
 
 Quality filtering: 
 The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.

WikiPage filtering.py modified by Sarah Bourlat

Sarah Bourlat — Mon, 23 Jul 2012 13:52:32 -0000

--- v1
+++ v2
@@ -1,4 +1,6 @@
-filtering.py (Quality filtering): 
+(filtering.py) [https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/filtering.py]
+
+Quality filtering: 
 The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output.
 
 [testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s

WikiPage filtering.py modified by MV2012

MV2012 — Fri, 20 Jul 2012 14:46:09 -0000

filtering.py (Quality filtering): The sequence data in FASTA format were then quality-filtered using a python script written for this purpose, filtering.py. This script finds records that are less than a certain length (specified by the user), empty records (no sequence), sequences which do not have the DNA alphabet (ambiguous or unambiguous), and excludes them from the final output file. The final number of records included in the output file is counted and the number specified in the output. [testfile1_filtering.fa] testing for DNA alphabet with records consisting of protein alphabet and "N"s [testfile2_filtering.txt] is a text file in a non-fasta format [testfile3_filtering.fa] containing one record of >100bp and another <100bp