Python include shell path filename

Question

Here is my code in shell and I include python command:

for file in `ls $FOLDER`
do
    echo "$file"
    var=`python -c "from Bio import SeqIO, SeqUtils; import os; rec = SeqIO.read("**$FOLDER/$file**", 'fasta'); SeqUtils.xGC_skew(rec.seq, 220000)" `
done

And I do not know how to make python recognize my file name

Are you getting any error? If yes, please add the error output in the question. — Shipra, Oct 29 '19 at 11:09
Here is the error: Traceback (most recent call last): File "", line 1, in File "/home/criuser/anaconda2/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 671, in read raise ValueError("More than one record found — Ran AJ, Oct 29 '19 at 11:12
It is like it does not see my file and I do not know how to tell it '$FOLDER/$file' in a python way — Ran AJ, Oct 29 '19 at 11:13

score 1 · Answer 1 · answered Oct 29 '19 at 11:23

You need to escape the double quotes in the python code:

for file in `ls $FOLDER`
do
    echo "$file"
    var=`python -c "from Bio import SeqIO, SeqUtils; import os; rec = SeqIO.read(\"$FOLDER/$file\", 'fasta'); SeqUtils.xGC_skew(rec.seq, 220000)" `
done

score 0 · Answer 2 · answered Oct 29 '19 at 15:03

I see some common shell mistakes:

Don't parse ls. Use
```
for file in "$FOLDER"/*; ...
```
Use $(...) instead of `...` -- easier to read, easier to nest. Reference
Get out of the habit of using ALLCAPS variable names, leave those as reserved by the shell. One day you'll write PATH=something and then wonder why your script is broken.

Python include shell path filename

2 Answers2