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0

I have been using the following bash command to process files (using another python script ~/$HOME/quality_filter.py). The files come in pairs i.e. R1 ans R2 files
eg.

MK2_S34_L001_R1_001.fastq, MK2_S34_L001_R2_001.fastq,

MK3_S87_L001_R1_001.fastq, MK3_S87_L001_R2_001.fastq

Where M2 and M3 are the sample names, the _S34_ and _S87_, are different for each sample and _R1_ and _R2_ are R1 and R2 respectively.

for FNAME in $IN_DIR/*_S*_L001_R1_001.fastq

do

   FILE=${FNAME##*/}

   SAMPLE=${FILE%*_S*_L001_R1_001.fastq}  

   mkdir $OUT_DIR/${SAMPLE}/

   COMMAND="python ~/$HOME/quality_filter.py -1 $IN_DIR/${SAMPLE}_S*_L001_R1_001.fastq -2 $IN_DIR/${SAMPLE}_S*_L001_R2_001.fastq -q 26" 

   echo $COMMAND >> $OUT_DIR/${SAMPLE}/QualityFiltering.sh

   cd $OUT_DIR/${SAMPLE}/

   sh $OUT_DIR/${SAMPLE}/QualityFiltering.sh

done

The output: for each of the samples a folder is created and in it a script named QualityFiltering.sh
eg.

/M2/QualityFiltering.sh

/M3/QualityFiltering.sh

How can I write the same in python 3. Thanks

bash python3

share|improve this question

edited 12 mins ago

alex kiarie

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

add a comment
 | 

0

I have been using the following bash command to process files (using another python script ~/$HOME/quality_filter.py). The files come in pairs i.e. R1 ans R2 files
eg.

MK2_S34_L001_R1_001.fastq, MK2_S34_L001_R2_001.fastq,

MK3_S87_L001_R1_001.fastq, MK3_S87_L001_R2_001.fastq

Where M2 and M3 are the sample names, the _S34_ and _S87_, are different for each sample and _R1_ and _R2_ are R1 and R2 respectively.

for FNAME in $IN_DIR/*_S*_L001_R1_001.fastq

do

   FILE=${FNAME##*/}

   SAMPLE=${FILE%*_S*_L001_R1_001.fastq}  

   mkdir $OUT_DIR/${SAMPLE}/

   COMMAND="python ~/$HOME/quality_filter.py -1 $IN_DIR/${SAMPLE}_S*_L001_R1_001.fastq -2 $IN_DIR/${SAMPLE}_S*_L001_R2_001.fastq -q 26" 

   echo $COMMAND >> $OUT_DIR/${SAMPLE}/QualityFiltering.sh

   cd $OUT_DIR/${SAMPLE}/

   sh $OUT_DIR/${SAMPLE}/QualityFiltering.sh

done

The output: for each of the samples a folder is created and in it a script named QualityFiltering.sh
eg.

/M2/QualityFiltering.sh

/M3/QualityFiltering.sh

How can I write the same in python 3. Thanks

bash python3

share|improve this question

edited 12 mins ago

alex kiarie

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

add a comment
 | 

I have been using the following bash command to process files (using another python script ~/$HOME/quality_filter.py). The files come in pairs i.e. R1 ans R2 files
eg.

MK2_S34_L001_R1_001.fastq, MK2_S34_L001_R2_001.fastq,

MK3_S87_L001_R1_001.fastq, MK3_S87_L001_R2_001.fastq

Where M2 and M3 are the sample names, the _S34_ and _S87_, are different for each sample and _R1_ and _R2_ are R1 and R2 respectively.

for FNAME in $IN_DIR/*_S*_L001_R1_001.fastq

do

   FILE=${FNAME##*/}

   SAMPLE=${FILE%*_S*_L001_R1_001.fastq}  

   mkdir $OUT_DIR/${SAMPLE}/

   COMMAND="python ~/$HOME/quality_filter.py -1 $IN_DIR/${SAMPLE}_S*_L001_R1_001.fastq -2 $IN_DIR/${SAMPLE}_S*_L001_R2_001.fastq -q 26" 

   echo $COMMAND >> $OUT_DIR/${SAMPLE}/QualityFiltering.sh

   cd $OUT_DIR/${SAMPLE}/

   sh $OUT_DIR/${SAMPLE}/QualityFiltering.sh

done

The output: for each of the samples a folder is created and in it a script named QualityFiltering.sh
eg.

/M2/QualityFiltering.sh

/M3/QualityFiltering.sh

How can I write the same in python 3. Thanks

bash python3

share|improve this question

edited 12 mins ago

alex kiarie

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

for FNAME in $IN_DIR/*_S*_L001_R1_001.fastq

do

   FILE=${FNAME##*/}

   SAMPLE=${FILE%*_S*_L001_R1_001.fastq}  

   mkdir $OUT_DIR/${SAMPLE}/

   COMMAND="python ~/$HOME/quality_filter.py -1 $IN_DIR/${SAMPLE}_S*_L001_R1_001.fastq -2 $IN_DIR/${SAMPLE}_S*_L001_R2_001.fastq -q 26" 

   echo $COMMAND >> $OUT_DIR/${SAMPLE}/QualityFiltering.sh

   cd $OUT_DIR/${SAMPLE}/

   sh $OUT_DIR/${SAMPLE}/QualityFiltering.sh

done

share|improve this question

edited 12 mins ago

alex kiarie

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

share|improve this question

edited 12 mins ago

alex kiarie

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges

asked 53 mins ago

alex kiariealex kiarie

3055 bronze badges