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Commit 492334d2 authored by adrien's avatar adrien
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clean repo errors and reduce size of datasets

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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
# C extensions
*.so
*.c
*.o
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml
# Translations
*.mo
*.pot
# Django stuff:
*.log
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# do not git test folder content and quade executable
/test/local_dataset/
/src/Quade
/
Conf.txt 0 → 100644
View file @ 492334d2
#########################################################################################
# #
# QUADE CONFIGURATION FILE #
# #
#########################################################################################
# Values can by customized with users values, but the file template must remain unchanged, otherwise the program will not be able to load default values.
# Please follow the following recommendations :
# - File path should be indicated as absolute path preferably and should not contain blank spaces
# - Values identified with '**' in the descriptor are not recommended to be modified
##########
[quality]
##########
# Minimal mean quality of the index to consider a read pair valid (between 0 and 40). 0 if no filtering requested. (INTEGER)
mean_qual : 30
# Minimal quality for one base of the index to consider a read pair valid. 0 if no filtering requested. (INTEGER)
minimal_qual : 20
# Quality format associated with reads autorized values are : solexa-old, solexa-old or phred. See HTSeq documentation for more details. (STRING)
qual_scale : phred
##########
[fastq]
##########
# Path to the fastq files containing non demultiplexed sequences. Since fastq splited in several chunks of data a list of fastq can be given for each categories
# chunks need to be indicated in the same order in all categories.
# list of path to chunks of fastq file containing the forward insert sequencing reads (usually R1)
seq_R1 : ./fastq/R1_001_100000.fastq.gz ./fastq/R1_002_100000.fastq.gz ./fastq/R1_003_100000.fastq.gz
# list of path to chunks of fastq file containing the reverse insert sequencing reads (usually R3)
seq_R2 : ./fastq/R3_001_100000.fastq.gz ./fastq/R3_002_100000.fastq.gz ./fastq/R3_003_100000.fastq.gz
# list of path to chunks of fastq file containing the first index reads (usually R2)
index_R1 : ./fastq/R2_001_100000.fastq.gz ./fastq/R2_002_100000.fastq.gz ./fastq/R2_003_100000.fastq.gz
# list of path to chunks of fastq file containing the second index reads (usually R4) [if double indexing only]
index_R2 : ./fastq/R2_001_100000.fastq.gz ./fastq/R2_002_100000.fastq.gz ./fastq/R2_003_100000.fastq.gz
##########
[index]
##########
# At the exception of index 1 which is mandatory, indicate by a boolean if the index is to be used or not.
# If not you can leave the start and end sections empty, else indicate the start and end positions within in index read using 0 base coordinates
# Sample index 1 start and end 1 based coordinates [MANDATORY] (INTEGERS)
index1_start : 1
index1_end : 6
# Sample index 2 True if double indexing only (BOOLEAN)
index2 : False
# Sample index 2 start and end 1 based coordinates (INTEGERS)
index2_start : 1
index2_end : 6
# Molecular index 1 True if stochastic index was added after sample index 1 (BOOLEAN)
molecular1 : False
# Molecular index 1 start and end 1 based coordinates (INTEGERS)
molecular1_start : 6
molecular1_end : 6
# Molecular index 2 True if if double indexing only and stochastic index was added after sample index 2 (BOOLEAN)
molecular2 : False
# Molecular index 2 start and end 1 based coordinates (INTEGERS)
molecular2_start : 6
molecular2_end : 6
##########
[output]
##########
# Write fastq files containing reads whose sample is undetermined
write_undetermined : True
# Write separate fastq files for each sample containing reads whose index has a low quality
write_fail : True
# Write a txt report
write_report : True
###############################
#  SAMPLE DEFINITIONS  #
###############################
# It is possible to include as many independant sample as required by duplicating a entire sample section and incrementing the id number in the sample section name
# All sample name and index have to be uniq
[sample1]
# basename that will be used to prefix the read files NO BLANK SPACE IN NAME (STRING)
name : S1
# Index sequences associated with the sample.Index 2 is used only in case of double indexing (STRING CONTAINING ONLY A T C G)
index1_seq : ACAGTG
index2_seq : ACAGTG
[sample2]
name : S2
index1_seq : CTTGTA
index2_seq : CTTGTA
[sample3]
name : S3
index1_seq : AGTCAA
index2_seq : AGTCAA
[sample4]
name : S4
index1_seq : GTGAAA
index2_seq : GTGAAA
[sample5]
name : S5
index1_seq : TGACCA
index2_seq : TGACCA
[sample6]
name : S6
index1_seq : CAGATC
index2_seq : CAGATC
[sample7]
name : S7
index1_seq : GCCAAT
index2_seq : GCCAAT
[sample8]
name : S8
index1_seq : CGATGT
index2_seq : CGATGT
LICENSE 0 → 100644
View file @ 492334d2
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README.md 0 → 100644
View file @ 492334d2
Quade
=====
Demultipler for fastq file based on index sequence including a PHRED quality filter
IN DEVELOPMENT
doc/Dev_notebook.ipynb 0 → 100644
View file @ 492334d2
{
"metadata": {
"name": "Dev_notebook"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Quade Development Notebook\n",
"\n",
"## Creation : 2015 / 01 / 07\n",
"\n",
"### Adrien Leger [adrien.leger@gmail.com](adrien.leger@gmail.com)\n",
"\n",
"###\u00a0Purpose\n",
"\n",
"* Parse chunks of non demultiplexed paired end fastq files (R1 R2 and Index 1 [and Index 2])\n",
"* Reads had to be attributed to the corresponding sample based on index correspondance\n",
"* Reads may be filtered based on the PHRED quality of the index read \n",
"* Finally the program had to handle stochastic molecular index that may be included in the index read\n",
"\n",
"###\u00a0Dependencies\n",
"\n",
"* Python 2.7+ (but not python3 due to Biopython incompatibility)\n",
"* Biopython 1.65+\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from Bio import SeqIO\n",
"import gzip"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can use either uncompressed fastq"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"in_R1 = gzip.open(\"./test/C01_R1.fastq.gz\", \"r\")\n",
"in_R2 = gzip.open(\"./test/C01_R2.fastq.gz\", \"r\")\n",
"in_R3 = gzip.open(\"./test/C01_R3.fastq.gz\", \"r\")\n",
"\n",
"R1 = SeqIO.parse(in_R1, 'fastq-sanger')\n",
"R2 = SeqIO.parse(in_R2, 'fastq-sanger')\n",
"R3 = SeqIO.parse(in_R3, 'fastq-sanger')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"in_R1 = open(\"./test/C01_R1.fastq\", \"r\")\n",
"in_R2 = open(\"./test/C01_R2.fastq\", \"r\")\n",
"in_R3 = open(\"./test/C01_R3.fastq\", \"r\")\n",
"\n",
"R1 = SeqIO.parse(in_R1, 'fastq-sanger')\n",
"R2 = SeqIO.parse(in_R2, 'fastq-sanger')\n",
"R3 = SeqIO.parse(in_R3, 'fastq-sanger')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 13
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print(next(R1, None))\n",
"print(\"\")\n",
"print(next(R2, None))\n",
"print(\"\")\n",
"print(next(R3, None))"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"ID: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180\n",
"Name: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180\n",
"Description: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180 1:N:0:\n",
"Number of features: 0\n",
"Per letter annotation for: phred_quality\n",
"Seq('CTGCAACTTACCTCCGGGATGGTCCAGACCCACGTCACCACCCCCGGCTCCATA...GGA', SingleLetterAlphabet())\n",
"\n",
"ID: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180\n",
"Name: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180\n",
"Description: HWI-1KL149:87:HA58EADXX:1:1101:1340:2180 2:N:0:\n",
"Number of features: 0\n",
"Per letter annotation for: phred_quality\n",
"Seq('GCCAAT', SingleLetterAlphabet())\n",
"\n",