dridk / abif Goto Github PK
View Code? Open in Web Editor NEWCommand line tool to read Applied Biosystems Genetic Analysis Data File Format
License: MIT License
Command line tool to read Applied Biosystems Genetic Analysis Data File Format
License: MIT License
Hi, Sacha!
The tool only displays exactly the first half of data contained in ab1 file. Data used for testing
./abif -l A_forward.ab1 | grep PLOC
produces output:
PLOC.1 1 4 2 809 1618 187161 0
PLOC.2 2 4 2 809 1618 188779 0
and we see that PLOC.1 contains 809 entries. Nevertheless
/abif -k PLOC.1 A_forward.ab1 | awk -F',' '{print NF}'
produces exactly the half:
405
Biopython's SeqIO though reads the same file correctly:
from Bio import SeqIO
seqHandle = SeqIO.parse("A_forward.ab1", "abi")
for seq in seqHandle:
print(len(seq.annotations['abif_raw']['PLOC1']))
Output:
809
Same goes for my data and for other fields (I checked DATA.9 and DATA.10) in ab1 files.
Try to resolve it.
The first half of data is read correctly though, I checked it.
Best wishes,
Kirill.
Installation
Is this s general issue of something wrong with my system? Can this be fixed?
make
g++ -c -pipe -O2 -std=gnu++11 -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_GUI_LIB -DQT_CORE_LIB -I. -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -isystem /usr/include/libdrm -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp
main.cpp:5:10: fatal error: QtCore: No such file or directory
#include <QtCore>
...............^~~~~~~~
compilation terminated.
Makefile:352: recipe for target 'main.o' failed
make: *** [main.o] Error 1
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.